Fellow mac user here. Read through your thread more or less, so I'm not sure if I understand everything of your situation correctly. The missing app support folder is odd, as far as I know, the app support folder creates itself when you start the game the 1st time. Did you do that after reinstalling? Otherwise I have no idea what's going on.
Also which version of JKA do you get from the app store? The newer (came out around 2013 which you can get on steam) or the original (around 2003)? The reason I ask, cause in the original you had separate folders for SP (Jedi Academy) and MP (Jedi Academy MP) in application support, but in the new you only get 1 folder, called "Jedi Academy" (naturally).
Anyway, all I'm trying to say here is that it's needless for you to try create the folder in application support (especially not with "Jedi Academy MP", as I think you have the newer version too), the computer does that automatically. If it doesn't, then perhaps you really don't need it, and what the guy said on the apple support forum is true. But I find that unlikely, cause you said that you had the application support folder before reinstalling the game. And you're installing the same version of the game now right? So from what I see you should try until you get the application support folder.
If you're convinced that you don't need/have application support, then I see 2 options here. 1st just put the MBII files next to your game, in your "normal" Jedi Academy folder. When I used the old version of the game, I could put the MBII folder next to the game itself and it worked, or I could put it in the application support as well, it didn't matter, mb2 ran in both cases (now I'm using the steam version and it only works if I put mb2 in the application support). And the second option is that you have to dig in the game app with "show package contents", and place the files somewhere there (I find this unlikely).
For the last few updates in mb2, I haven't used the launcher, so I don't know if it works at the moment for Macs (cause the 1st time the launcher came out, it worked, then there was a time that it didn't), but in my opinion it's a lot faster and easier to install manually. You put the downloaded files in the "MBII" folder and that's it.
Launching the mod is tricky as well, as Puppy said, you should use JKALaunch, and set that up correctly. I can write about that if you have problems with it, but from what I see, that's not an issue.
Hope you succeed, also 1 more advice. Only install the game in "Applications" if you install it in a custom place, you can get all kinds of problems.
