When I started on this core, keeping it completely compatible with the C64 was not my goal. In fact, I considered that a near impossibility, as the C128 itself is only like 99% compatible and not the 100% Commodore liked you to believe. It's much more than just a single byte of memory, for example, the VDC is available and usable from the C64 mode. Eye of the Beholder uses this, it runs in C64 mode, but uses the VDC and turbo modes on a C128. Somehow switching cores when doing a "go64" would make that impossible. Also, the C128 is architecturally so much like the C64, it would still need all the C64 hardware anyway.
Other changes impact features from the C64 core as well. The configurable turbo modes that the C64 core has are disabled. Setting it to 3x or 4x speed will crash the 8502 and VIC. I haven't figured out why yet.
Cartridges that work on a real C64 but not a C128 are bound to not work on the C128 core as it is now either, regardless of the "pure" C64 settings. (In hindsight the word "pure" is overpromising.. I should have thought about that a bit more). Not sure if the Action Replay is supposed to work on a real C128. If it does, I should look into that. But if it doesn't on a real C128, I consider this "works as intended" at the moment.
From a maintenance perspective it's indeed much better to have a single unified core. But right now, the C128 core is not ready for that as it would be downgrading the C64 experience. The burden on maintaining the C128 core is on me. When Sorgelig makes changes to the C64 core I'll merge them into the C128.
Maybe in time we can indeed merge these two into one core. But I don't think it would do the C64 core justice to do that now.