Three types of warnings:
1) Changing floors in a branch (branch = any uniquely named area, including the Tower itself, as well as each one-floor side dungeon)
2) Leaving a branch.
3) Winning the game.
So no, there is no difference in warning currently between changing floors in a branch when there is or is not a different branch entrance is present.
I think I understand what you meant now, sorry, you want a new one:
4) Changing floors in a branch, if another branch entrance is present.
I think I will also add an option to get rid of the warning types 1 and 2, but leave 3 and 4 has always on. Sound happy?