I'm not sure it would solve the problem. It's not that you would accidentally use RTG-chunky instead of bitplanes or use ten bitplanes instead of eight or whatever. You wouldn't accidentally use 080-only processor instructions either.
On the CPU-side I don't think it would be much of a problem, but if SuperAGA has any overlapping bits/registers compared to real AGA (for example, using unused bits in the current registers), then there most certainly could be problems. Adding a RTG chunkybuffer is not a problem, but reimplementing AGA with added bells and whistles is, at least for me.
The problem is that you would have to trust the reimplementation to be true to the original. The same happens with WinUAE and the real hardware.
To be honest, I have way more trust in WinUAE than in any reimplementation. Mainly because the goals are different, WinUAE tries to be as close to the original hardware as possible where as Apollo Core wants to be compatible but also add a lot of features.
But I feel this conversation isn't moving anywhere, the Apollo Core in it's current form just isn't for me.