Anyway to split apps sharing an UID?
I don't think it's possible to change this without recompiling the ROM. You can't change the UID of apps after they're installed because they won't be able to access their files any more, and because it will confuse the app permissions system.

Maybe there's some other way around the problem with Xposed, but I don't know about that. It might be possible for an Xposed module to detect the exact call the package is making (to distinguish it from the calls made by other packages in the same process), and mark it for AFWall to allow it. That way you wouldn't need to split up the apps at all.

An alternative might be to find where it's trying to send traffic to, and whitelist that address for that process. Again, this would solve the specific symptom without splitting the apps. If it's the captive portal detection, it's probably http://client.android.com/generate_204.