I was looking at how the installer uses basically a bindiff to patch existing modules. It may be faster if you use a bindiff to patch and empty bsa, extract it and then overwrite the changes into the being built bsa. It won't be quite as accurate sha/md5 as the other but would allow people with slightly different bsa's to use the mod. For the life of me I can't figure out why some of my bsa's didn't match the md5s of the diff files, I updated them to the latest patch, perhaps cause they were disk installs, and some gfwl (although my zeta patched perfectly).
The downside to this approach is that, if people have slightly corrupt bsa's, it could create some support issues.
My 2 cents.
(BTW I know how to rebuild bsa's, is there a possibility in the interim to get just the changed files, in like a zip or something) I'm not certain why it seems so closely guarded in the installer.