Kara no Kyoukai and Tsukihime are *NOT* the same universe. They are all part of the greater Nasuverse, but they are not the same universe. At all. Fate, KnK, and Tsukihime are the three sub-universes that make up most of the greater Nasuverse. (There's also stuff like DDD in there, but then we're getting real in-depth - for all intents and purposes, those are the three that "matter.")
But we know Touko exists in the Tsukihime universe. She's referenced by Aoko in the canon.
I want to know why they aren't the same thing, though - there's no actual canon saying that they aren't happening at the same time, and Aoko even shows up in KnK if you're paying attention (she pretends to be Touko when Ryougi is in the hospital). There's absolutely no reason that they can't be happening at the same time, especially if Ryougi can be summoned at all. My understanding of Kara no Kyoukai was that it's like Tsukihime: Gaiden - KnK gives much more insight into the mechanics and the workings of the Tsukihime world, and actually helps to explain some of the things in Melty Blood in particular that I didn't understand.
Additionally, Azaka really is nothing like Akiha if you take into account the fact that she's quoted by Shiki to be "unrealistically strong" - she's much more a brawler than Akiha is in the canon, and I think she'd play VERY differently in a fighting game. Additionally, even though her character design is SIMILAR, it's not really identical imo - Azaka is definitely much more girlish than Akiha is, with Akiha having a bit more of a dignified look.
The only one that I think is a bit of a stretch would be F/SN characters in Melty Blood, since most of them are never referenced in the source material, and Fuyuki city isn't mentioned at ALL. However, Touko is referenced by Aoko, and obviously Ryougi is there, so who's to say they aren't happening simultaneously?