You are quite right. It will just point the rear of the diff down a bit, not helping the drive line angle any. It will only lower the inner part of the CV's down slightly. And yes, on a T100 it may interfere with the rear crossmember. I don't know why anybody would put one of those kits on this type of suspension.

The simple fix to limit the CV boot wear is to install manual hubs and unlock them when you aren't going to be needing 4wd. Even better would be to un-crank your torsion bars a bit.

'97 4Runner, '06 F350, '86 4Runner, '05 WR450
http://home.4x4wire.com/erik