Originally Posted by snarkophilus
I don't think that's to do with the key, but rather than it's installed as a different app with a different user ID.
For example, on my T1 /data/data/com.sony.drbd.ebook.reader is owned by UID 10006 (and GID 10006) but /data/data/com.sony.drbd.ebook_mod.reader is owned by UID 10046 (and GID 10006). Under /data/data/com.sony.drbd.ebook.reader there's a directory called shared_prefs and a file in there called com.sony.drbd.ebook.reader_preferences.xml and the permissions on that file are read/write for the user and group, but no access for everyone else.
Yes, but all apps sharing a user ID must be signed with the same key
Perhaps the actual file permissions can be changed, but then I'd have to make sure they aren't overwritten.