Aredub,
He had it covered under warranty. I'm not at all surprised that the dealer tried to (and probably succeeded in) raping the warranty company.
Now if it wasn't covered under any warranty, then I'd be concerned...
(Hi! My name is Ben Dover, and I'm the service manager at XYZ Subaru. Customer has a bad tranny, and it'll cost $4100 to replace. OK? Great then. Hangs up phone, then snickers)
VK