I've replaced the default Sims University with http://modthesims.info/d/520269]Pinewood University[/url] from MTS because the default is way too huge and empty for my tastes, but I have a hard enough time jamming the EP lot types into neighborhoods without adding a homeworld university. Sims University wasn't in WorldCaches to begin with and I cleared ScriptCache as usual when installing. The game doesn't seem to have a problem with loading the world, but when I was setting up Register settings in a new save I noticed Sims University appears in the "Disabled Tourist Worlds" menu twice.
Also, I was unable to get the menu to open again after selecting both universities. No script error logs were generated. Is this a harmless visual glitch, or likely to lead to BFBVFS?
(I haven't looked at Traveler's menus yet, but I wouldn't be surprised if the same thing happens there.)

I have MasterController, Register, Traveler, Overwatch, ErrorTrap and Woohooer installed (along with Awesome), but not Careers if that would make a difference.

Wait, I just thought of something. The old file was in the folder as original Sims University.world. I'm going to try changing the file extension of the old one and see if that makes the duplicate go away- when I replaced the other EA worlds with the routing fixes, I had moved the originals to a separate folder instead of renaming, so I haven't actually seen how Register/Traveler behave with multiple .world files hanging around.

That's what I was going to ask, Pinewood University is intended to replace the University Life world in your EP game installment, without renaming the Original file extension the Univeristy Life and Pinewood University coincide beside each other.

It's not so much how Traveler and Register will behave with multiple *.world files, its more likely how the Game Core will react when you decide to enroll some Sims to a Major, which world will it take as the game sees duplicate Wolds ID in your system. Think it will go screwy.

Read the How Install section on the creators mods info description over at MTS, if you not already done that.