IBM clones transformed the market because the PC standard (with MS-DOS) became a commodity, which meant you could swap software and data between machines from different manufacturers and Compaq made sure could buy the hardware via a network of dealers, like a car - something Apple originally innovated, and the S100 scene experimented with, but never quite mastered.
The compatibility was a Really Big Deal at the time. It was far more important to users than the very obvious technical limitations of the hardware. Not only could you share data, but you could take your disks to a different office with different hardware from a different clone maker and still get work done.
Incidentally, Unix would never have happened in this market because the shell syntax (all of them...) is far too hostile for most users.
Shiraz Shivji from both the C64 and the Commodore 900 team ended up leaving with Tramiel when he bought the corpse of Atari. He ended up being the architect of the Atari ST.