Both sold PC clones, and I suspect if those lines had been very successful $$ wise they may have attempted to do something like what you said. Or more likely some kind of Amiga-esque runtime environment overtop of (choke, gag) DOS. We would have all screamed bloody murder about it though.
In any case, AmigaOS and Atari's TOS were pretty heavily tied into the 68k ecosystem. Switching ISAs would have really been starting over.
Moving from 68k to PowerPC almost killed off Apple, and they were many multiples the size of Commodore & Atari.
Myself I made the switch from 68k Atari ST to 486+early-Linux in 1992. At that point we were already doing Unix-like things on the Atari (MiNT with unix ports, or, on the 030/020 systems, full NetBSD Unix), so it felt like a natural jump. SVGA + a 486 was a pretty damn competitive workstation-like system at that point.