How to replace email notifications with custom layout?

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This is example of code which help you to overwrite email notifications template

add_filter('bp_better_messages_overwrite_email', 'override_messages_emailer', 10, 4);

function override_messages_emailer( $bool, $user_id, $thread_id, $messages ){
    $gmt_offset = get_option('gmt_offset') * 3600;

    /**
     * Get user which will receive email
     */
    $user = get_userdata( $user_id );

    /** Getting subject  */
    $subject = $messages[0]->subject;

    $email_subject = '[' . get_bloginfo('name') . '] You have unread messages:'  . $subject;
    $thread_url    = esc_url(BP_Better_Messages()->functions->get_link($user_id) . '?thread_id=' . $thread_id);
    /**
     * Composing html messages list
     */
    $messageHtml = '<table style="margin: 0 0 20px!important;width: 100%;"><tbody>';
    $last_id = 0;
    foreach ($messages as $message) {
        $sender = get_userdata($message->sender_id);

        $timestamp = strtotime($message->date_sent) + $gmt_offset;
        $time_format = get_option('time_format');

        if (gmdate('Ymd') != gmdate('Ymd', $timestamp)) {
            $time_format .= ' ' . get_option('date_format');
        }

        $time = wp_strip_all_tags(stripslashes(date_i18n($time_format, $timestamp)));
        $author = wp_strip_all_tags(stripslashes(sprintf(__('%s wrote:', 'bp-better-messages'), $sender->display_name)));
        $message = wp_strip_all_tags(stripslashes($message->message));

        if ($last_id == 0 || $last_id != $sender->ID) {
            $messageHtml .= '<tr><td colspan="2"><b>' . $author . '</b></td></tr>';
        }

        $messageHtml .= '<tr>';
        $messageHtml .= '<td style="padding-right: 10px;">' . $message . '</td>';
        $messageHtml .= '<td style="width: 1px;white-space: nowrap;vertical-align: top;"><i>' . $time . '</i></td>';
        $messageHtml .= '</tr>';

        $last_id = $sender->ID;
    }

    $messageHtml .= '</tbody></table>';

    /**
     * Composing Email HTML
     */
    ob_start(); ?>
    <!doctype html>
    <html>
    <head>
        <meta name="viewport" content="width=device-width">
        <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
        <title>Simple Transactional Email</title>
        <style>
            /* -------------------------------------
                INLINED WITH htmlemail.io/inline
            ------------------------------------- */
            /* -------------------------------------
                RESPONSIVE AND MOBILE FRIENDLY STYLES
            ------------------------------------- */
            @media only screen and (max-width: 620px) {
                table[class=body] h1 {
                    font-size: 28px !important;
                    margin-bottom: 10px !important;
                }
                table[class=body] p,
                table[class=body] ul,
                table[class=body] ol,
                table[class=body] td,
                table[class=body] span,
                table[class=body] a {
                    font-size: 16px !important;
                }
                table[class=body] .wrapper,
                table[class=body] .article {
                    padding: 10px !important;
                }
                table[class=body] .content {
                    padding: 0 !important;
                }
                table[class=body] .container {
                    padding: 0 !important;
                    width: 100% !important;
                }
                table[class=body] .main {
                    border-left-width: 0 !important;
                    border-radius: 0 !important;
                    border-right-width: 0 !important;
                }
                table[class=body] .btn table {
                    width: 100% !important;
                }
                table[class=body] .btn a {
                    width: 100% !important;
                }
                table[class=body] .img-responsive {
                    height: auto !important;
                    max-width: 100% !important;
                    width: auto !important;
                }
            }

            /* -------------------------------------
                PRESERVE THESE STYLES IN THE HEAD
            ------------------------------------- */
            @media all {
                .ExternalClass {
                    width: 100%;
                }
                .ExternalClass,
                .ExternalClass p,
                .ExternalClass span,
                .ExternalClass font,
                .ExternalClass td,
                .ExternalClass div {
                    line-height: 100%;
                }
                .apple-link a {
                    color: inherit !important;
                    font-family: inherit !important;
                    font-size: inherit !important;
                    font-weight: inherit !important;
                    line-height: inherit !important;
                    text-decoration: none !important;
                }
                #MessageViewBody a {
                    color: inherit;
                    text-decoration: none;
                    font-size: inherit;
                    font-family: inherit;
                    font-weight: inherit;
                    line-height: inherit;
                }
                .btn-primary table td:hover {
                    background-color: #34495e !important;
                }
                .btn-primary a:hover {
                    background-color: #34495e !important;
                    border-color: #34495e !important;
                }
            }
        </style>
    </head>
    <body class="" style="background-color: #f6f6f6; font-family: sans-serif; -webkit-font-smoothing: antialiased; font-size: 14px; line-height: 1.4; margin: 0; padding: 0; -ms-text-size-adjust: 100%; -webkit-text-size-adjust: 100%;">
    <table border="0" cellpadding="0" cellspacing="0" class="body" style="border-collapse: separate; mso-table-lspace: 0pt; mso-table-rspace: 0pt; width: 100%; background-color: #f6f6f6;">
        <tr>
            <td style="font-family: sans-serif; font-size: 14px; vertical-align: top;">&nbsp;</td>
            <td class="container" style="font-family: sans-serif; font-size: 14px; vertical-align: top; display: block; Margin: 0 auto; max-width: 580px; padding: 10px; width: 580px;">
                <div class="content" style="box-sizing: border-box; display: block; Margin: 0 auto; max-width: 580px; padding: 10px;">

                    <!-- START CENTERED WHITE CONTAINER -->
                    <table class="main" style="border-collapse: separate; mso-table-lspace: 0pt; mso-table-rspace: 0pt; width: 100%; background: #ffffff; border-radius: 3px;">

                        <!-- START MAIN CONTENT AREA -->
                        <tr>
                            <td class="wrapper" style="font-family: sans-serif; font-size: 14px; vertical-align: top; box-sizing: border-box; padding: 20px;">
                                <table border="0" cellpadding="0" cellspacing="0" style="border-collapse: separate; mso-table-lspace: 0pt; mso-table-rspace: 0pt; width: 100%;">
                                    <tr>
                                        <td style="font-family: sans-serif; font-size: 14px; vertical-align: top;">
                                            <p style="font-family: sans-serif; font-size: 16px; font-weight: bold; margin: 0; Margin-bottom: 15px;">Hi <?php echo $user->display_name; ?>,</p>
                                            <p style="font-family: sans-serif; font-size: 14px; font-weight: normal; margin: 0; Margin-bottom: 15px;">You have unread messages: "<?php esc_attr_e($subject); ?>"</p>
                                            <?php echo $messageHtml; ?>
                                            <p style="font-family: sans-serif; font-size: 14px; font-weight: normal; margin: 0; Margin-bottom: 15px;"><a href="<?php echo $thread_url; ?>">Go to the discussion</a> to reply or catch up on the conversation.</p>
                                        </td>
                                    </tr>
                                </table>
                            </td>
                        </tr>

                        <!-- END MAIN CONTENT AREA -->
                    </table>

                    <!-- START FOOTER -->
                    <div class="footer" style="clear: both; Margin-top: 10px; text-align: center; width: 100%;">
                        <table border="0" cellpadding="0" cellspacing="0" style="border-collapse: separate; mso-table-lspace: 0pt; mso-table-rspace: 0pt; width: 100%;">
                            <tr>
                                <td class="content-block" style="font-family: sans-serif; vertical-align: top; padding-bottom: 10px; padding-top: 10px; font-size: 12px; color: #999999; text-align: center;">
                                    <span class="apple-link" style="color: #999999; font-size: 12px; text-align: center;"><a href="<?php echo home_url(); ?>"><?php echo get_bloginfo('name');  ?></a></span>
                                </td>
                            </tr>
                        </table>
                    </div>
                    <!-- END FOOTER -->

                    <!-- END CENTERED WHITE CONTAINER -->
                </div>
            </td>
            <td style="font-family: sans-serif; font-size: 14px; vertical-align: top;">&nbsp;</td>
        </tr>
    </table>
    </body>
    </html>
    <?php
    $content = ob_get_clean();

    /*
     * Configure wp_mail to send as html and sending
     */
    $content_type = function() { return 'text/html'; };
    add_filter( 'wp_mail_content_type', $content_type );
    wp_mail( $user->user_email, $email_subject, $content );
    remove_filter( 'wp_mail_content_type', $content_type );


    // If true is returned there plugin will not send email itself, if false is returned it will send.
    return true;
}
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