The "We hope you enjoy your new site., Thanks!" message is actually within WordPress itself (and not cPanel) - in particular in these files:
wp-admin/includes/schema.php:We hope you enjoy your new site. Thanks!
wp-admin/includes/upgrade.php:We hope you enjoy your new site. Thanks!
wp-includes/ms-functions.php:We hope you enjoy your new site. Thanks!
and the appropriate wp-content/languages/* files.
You'll either need to modify those files on each existing installation for future upgrades (but that might be overwritten by WordPress itself) and the installation script. However, it looks like the toolkit downloads directly from wordpress.org (see the documentation
- yes, it's on Plesk's site, but it is actually developed by them) using wp-cli so that won't be possible.
The only way I can think of possibly working around it is to change the files in /usr/local/cpanel/3rdparty/wp-toolkit/plib/vendor/wp-cli/vendor/wp-cli/wp-cli/php/ to set the core download url
to your own copy of the WordPress installation.... But that's nasty/horrible as anything and I wouldn't attempt that myself even if I was the only one using it (as keeping the install file up to date and hoping that WP-Toolkit/cPanel doesn't overwrite my changes - urgh!)