I hope you do understand that it would not damaging compatibility with 95-98, but with windows 8. The class of programs that this is for runs fine on Windows 8, because they are not executing legacy code for 95-98. But the check for 95-98 would return true for windows 9. So the legacy code will be executed, probably breaking stuff because the API has changed a lot.
I do understand that. We'd be talking about programs built in the 95-98 era however, and the majority would not be in current use. The biggest exception would be enterprise, though if they're upgrading to a recently released Windows version they'd (hopefully!) be using more modern software too.
At the end of the day, we're still only guessing at Microsoft's rationale. Esoteric compatibility issues seem lower down the list from issues like breaking away from the Windows 8 name (which has accumulated negative association in the public view).
Until Microsoft says for sure, it's just a bit silly to make the claim as fact.
And you're discounting company-internal products that were built in the 95-98 era, then updated when new business regulations came out, but were never rewritten in a modern language and the company wouldn't spend time and money to port them to Windows 9 when they worked fine on every previous version -- they'll just wait until a newer version of Windows fixes the problem or Microsoft very forcibly drop support for 8 completely.
And as for some evidence this is the case: https://searchcode.com/?q=if%28version%2Cstartswith%28%22win...