I'm not sure I understand which one you're talking about.
NO custom passwords.
It's called custom password because the user sets it on registration instead of WP generating it for them.
It is the email they receive when they FIRST set their password THEMSELVES
Ok, so they set their password... Where? On the registration page or after clicking on a link they got by email to go set their password?
I want to know where the content of that email is populated from
I already pointed you to the one that s2Member has an interface for, which is the email they get on signup, setting their preferred password during signup. Did you see that in your configuration? WP Admin > s2Member > General Options > Email Configuration > New User Email
What does the email you want to change, say by default? Maybe that'll help me identify which you're talking about.