FWIW, x86 has always been a pretty moving target with many instruction set extensions, especially for various SIMD features. But even something fundamental like `popcnt` has a separate CPUID flag, even though Intel considers it part of SSE4.2.

Targeting the broadest possible variant of x86-64 limits you to SSE2, which is really not very capable outside of fairly basic float32 linear algebra. Great for video games, but not much else.

Also keep in mind that .NET originated right at the cusp of x86-64, which again is a whole different architecture from its 32-bit predecessor. Most native apps used to ship separate binaries for years.

And of course, I think Microsoft was aware of their intrinsic dependency on other companies, especially Intel. I can see how the promise of independence was and is enticing. They also weren't interested in another dependency on Sun/Oracle/whoever maintains Java at the moment. While Windows on ARM64 is still in a weird spot, things like .NET are useful in that transition.

Lastly, the CLR is different from the JVM in a number of interesting ways. The desktop experience with the JVM is not great, and Java is a very bad language. It makes sense to do your own thing if you're Microsoft or Apple.