What happens if i assign let's say 2 different (custom) roles to a user that both of which have the same (custom) capability?
I am pretty sure that nothing would happen other than the user would have the capability in question.
Think about it. The default Roles share many capabilities-- Authors, Editors, and Administrators all have
edit_posts, for example. All roles (usually) have
The same system manages both default and custom roles/capabilities, so there really should be no problem.