Nope. The C64 emulator dev team obtained the legal rights for the project, and also obtained the rights for the ROM packs they published as well.
Apple are just being arbitrary with which emulators they approve (Sega) vs the ones they reject (C64).
I don't think so. The Sega stuff may be an emulation but it doesn't run arbitrary 3rd party code, which I think is the distinction.
The C64 emulator is a full emulator that can be used to run apps not obtained through the app store. That's why Apple are rejecting it. The problem is, whilst a c64 emulator is clearly not comparable to a Java VM, from Apples POV it's probably hard to create a clear descriptive distinction, so they just go with the blanket approach.
That said, I'd be all over this if Apple weren't being so pissy about using the SDK to run VMs.