Jacking up the car to install the strut bar is one of the ways they used to install the strut bars. But I don't think the e46's relatively new chassis required that..
AFAIK, it wouldn't affect the camber and alignment, maybe just marginal.
Damaged / deformed strut towers can be repaired.. Since u didn't notice any significant damage to it, I'm assuming it could be just minor...
Maybe you can come by for TT andwe can see see what's wrong it.. Can help u fit it if I think can be done...