This is an interesting dichotomy: analogue vs digital - but I think there’s a third leg to it which is DSP. When your floor is a 1 MHz 6502 and you have a DSP running at many many multiples of that, you can mimic analogue circuits almost perfectly, with identical latency, but better reliability, serviceability, and cheaper parts. The key thing to remember here is that the 2040 is more like a DSP emulating the
signals than a regular pi emulating the
system. Something as simple as a c64 it should be possible to emulate with DSP indistinguishable from discrete circuits.
The key latencies you describe (frame buffer, audio) aren’t really an issue in the DSP scenario. Also, non linear components like the SID are going to be harder to reimplement in discrete circuits and in fact I’d expect DSP would do better.
DSP wins every time in all domains. Problem is you need to have a much more fine-grained knowledge of the physical underpinnings of the system, not just the system itself.