You can fail missions ?...I believe though that for example the Arcane University could make you go anywhere in the map, since they are the HQ of the Mages Guilds. BTW I think the other guilds should also have their version of the Arcane University.
You can't YET because there is ZERO flexibility in guild questlines, or in fact any questline.
As for the arcane university, they may be able to send you all over but they should only do that for MAJOR issues and NOT "bring me that book back". Smaller issues should still be the responsibilities of the Mages Guild hall in the district. Opening a NEW Guild hall in a town that doesn't have one yet, THAT would be a major issues worth sending you all the way over the map.
As for a version of the AU for the other guilds, for SOME yea but not for all.
-The Imperial Legion, they could have a "boot camp" so to say you're actually required to pass if you want to sign up as a soldier
-The Fighters Guild, they are pretty much just mercenaries, they can take anything that can fight, but military training as a background could be preferred so "graduating" from IL Boot camp can bring you some points.
-The thieves guild should not be that organized to begin with, I'd rather see them like mob families each controlling their own territory. They could at max have a meeting place for the mob bosses.
-If there are trades and commerce guilds again (BTW, guild DOES mean exchanging goods and services) they could have a central HQ of course, that would probably be located in the primary harbor or inland trade route town.
-Cults and churches can of course have central temples but again each is primary responsible for it's district. They can of course request help from others so there could be longer distances involved.
-Any underground operation would be very unlike to have a big open meeting place or central HQ as their whole existence has to stay hidden, they'd at max would proabably have, like the thieves, a central meeting place.