Closing as won't fix. We can revisit if GNU diff ever supports generating git-style patches.

Quilt is relying on diff and patch to generate and apply the changes, respectively. The only way to save and restore file permissions is to use diff and patch utilities which support that.

The only patch file format which supports storing file permissions is the git-style patch format. GNU patch knows how to process the file permissions information contained in such patches already, so if you import a git-generated patch in quilt and never refresh it, file permissions will be handled gracefully (assuming you use a recent enough version of GNU patch).

GNU diff, on the other hand, is still not able to generate this patch format. This feature was added to the to-do list one month ago, so this might eventually happen. When this happens, it will be possible to add support to quilt with minimal effort.

Permissions are already restored on "pop" independently of the patch format or the diff and patch utilities, as "pop" restores the original files from a backup and the backup operation does already preserve file permissions.

I can't see how a generic hook for a custom post-push or post-pop script would be convenient here. You would have to write custom code for every patch which creates a file with non-standard permissions. You can already interleave quilt and other shell commands for the same result.