This is an excellent question!
A general answer to your first general question, along with the responses above, is that an airthrow ender is better for momentum most of the time, but there is always a more damaging alternative. However, you want to airthow unless you have a very specific reason to use another air combo ender. "200 more damage" usually is not a good enough reason to. A few example reasons are:
1. That 200 more damage will win the round for me.
2. This ender will set up a tech punish
3. This ender I am using will waste enough time to run out the opponent's HEAT bar
4. I am using Mech Hisui
Now for your more specific j2c quesiton with Warc: Yes, in the corner, as long as you can learn the timing, j2c ender is may be worthwhile. It does deal a little more damage as well as give around 30% more meter. As far as I can tell though, it's actually slightlly worse for momentum, but the extra damage and meter is a pretty good tradeoff.
I'd suggest optimizing the rest of your combo before worrying about the ender though. First off, a good start is 2a 2b 2c 5c jb(2 hits) jc djb(2 hits) jc throw. You need to delay the 2c after the 2b a little bit, but this is the standard warc combo to my knowledge. Feel free to peruse the Warc subforum here and ask about her for more specific information though, as I'm not a Warc expert.