As far as integrating GFX/Audio w/ DMA on the motherboard, even most modern x86 boards do this, with a bypass ability to upgrade, which the Amiga didn't really have.
Yeah, but there are lots of different motherboard chipsets, not to mention NVIDIA vs ATI chipset. So trying to hardware bang like the old days and spread you code is much harder not to mention the complexity of the newer hardware.
What might be cool is like a base line spec (like A500 was sort the base line for a long time)
Now, DirectX is pretty much the base line these days. You right your code to that and then it takes care of what ever hardware you're on. Or OpenGL might be similar.
The question would be would it be relevant to have a base line hardware spec (like A500) instead of a software one like D3D?
Basically, either one motherboard is chosen and all software is written for that or you come up with a spec and all hardware is made to that spec.
I'm guessing most the hardware banging days are gone. Evertyhing abstracted through software is much easier to program to. And there is so much power it hardly makes sense to do it any other way these days.