Remove unneeded exceptions in compare.sh

Over time, we have been better at addressing inconsistencies in the build, but the exceptions put in place in compare.sh have not been updated to reflect this.

This attempts to make sure we only keep those exceptions that are currently actually needed to verify a reproducible build (the primary usecase for the compare script these days).

I also discovered bugs in the script, where mismatches in a zip file did not make us report a failed comparison. I added extra code to make sure we always set the REGRESSION flag whenever we detect a problem.