"Ah, those who don't remember history."
It wasn't so simple... while some established brands avoided to clone exactly the IBM PC and made their own x86 computers with their versions of MS-DOS, probably to avoid litigation with IBM and hope in some form of lock-in, others, mostly "startups" in modern term, cloned the PC completely very early, reversing and/or re-implementing the BIOS also. No need to ask then for specific versions of MS-DOS and its applications, something very important for small, young companies.
Because software began very early to bypass MS-DOS and even BIOS for performance reasons (especially video stuff, being MS-DOS really to slow and cumbersone, and feature-limited) - and not only games. While MS Flight Simulator was often used as a test due to its complexity - what matter most was compatibility with software like Lotus 1-2-3, WordStar or Sidekick. For most of these companies, still in their infancy, coding, testing and supporting different systems was a real burden.
And probably also the diffusion of pirated software boosted the market for PC clones....