To get it to work, you'd need to re-sign the apk using the private key used by the application's developer.
Hmmm... We might need to remove /data/app support for theming, as it's a horrendous idea tbh, since it will break market signatures... You need to resign data apps, as they won't work with "broken" sigs, while system apps WILL work (hence this theming method works).
So I think what's best is that we remove /data/app theming support, though insertion of full signed APKs into /raw/data/app would be possible... But doing so needs a new sig, so anyone using the old original APK won't see the newo ne until packages database was purged of the old sig...
So summary? If app is on /data, don't go near it