I know about the Rebel fighter issue. We discussed this matter and actually are still discussing it. There are some hex-values in the XWINGALLIANCE.EXE file that set the ships placed in the hangar. However my programming knowledge is not that great yet as if I could do that.
As for the TIEs and such, I already have permission from Darksaber to use his updated TIE Fighters. However as there's a mesh limit for OPTs it'll only be one or two. However this and a bunch of other bugfixes will be part of version 2.0 which I'm going to do after my exams next month.
And finally, this hangar is subject to be used as your starting platform in the TIE Fighhter Total Conversion. Most of the battles, missions and sound conversions are already finished. It is only a matter of time until you can play original TIE Fighter in XWA(and XWAU) quality.