Yes, you could. See: WP Admin > s2Member > General > Email Config
"PHP Code: It is also possible to use PHP tags—optional (for developers). If you use PHP tags, please run a test email with
<?php print_r(get_defined_vars()); ?>. This will give you a full list of all PHP variables available to you in this email. The $user variable is the most important one. It's an instance of the WP_User class (e.g., $user->ID, $user->has_cap(), etc). Please note that all Replacement Codes will be parsed first, and then any PHP tags that you've included. Also, please remember that emails are sent in plain text format."
So you can have a conditional that checks the level and gives a very different message based on that.