I think your final "re-use animations for other models" reason is the best reason for this. Any model that uses the same skeleton can use these animations, and this gives you the option to only attach the animations you're actually using for that particular character - saving space in the .cached.dts file, which is a very minor benefit, in the process. Of course, only editing and exporting a single short sequence versus the entire series is good, too.I think exporting the animations as single animation files is the best way to handle it, this way you can exchange and fix single animations without touching the whole thing and also re-use animations for other models later.
By the way - I'm right! Nyah nyah!