It’s possible that the Quake 3 engine counts vertices differently, I don’t really have much experience with models:-P Other people have run into this limit though, so obviously it exists in some form. Actually, googling a bit it appears the limit is per object (and a model can contain several objects).
As far as I know there are no fundamental differences between ASE and MD3 — both look identical and have the same (low-ish) performance impact. Apparently MD3 can’t be used for very large structures though — 512 unit limit?. ASE can be edited more easily and it’s a “real” model format, supported by many programs, unlike MD3 which is only used in some games.
BTW, you can also use OBJ format, but this can be tricky to pull off
. There are a few more formats listed in the model selection window of Radiant; never heard of anyone using them for UrT though.