M68000 wasn't a minority architecture at the time Apple adopted it. It was a workstation workhorse. That's part of what justified the Lisa's $10,000 price in 1983. But a lot of it was margin and hence a year later 68000 Macs could be sold for less than a quarter that price but still offer incredible performance on a personal computer. By adopting a *nix based OS, Apple reduced most hardware compatibility issues to recompilation, performance of course being another matter.

As for the dark days of Apple in the PC market and the deaths of Commodore and Atari, my recollection is that it had more to do with the stock market crash of 1987 tightening access to capital and the S&L crisis that followed it creating a recession where downsizing was what corporations not empty-nesters did.