NTVDM requires Virtual 8086 mode in the processor. This doesn't exist in the 64-bit modes, requiring a software emulator. That is why OTVDM/WineVDM exist.

You can see all of this explained in the README for the very project you linked:

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How does it work?

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I never thought that it would be possible at all, as NTVDM on Win32 uses V86 mode of the CPU for fast code execution which isn't available in x64 long mode. However I stumbled upon the leaked Windows NT 4 sourcecode and the guys from OpenNT not only released the source but also patched it and included all required build tools so that it can be compiled without installing anything but their installation package. The code was a pure goldmine and I was curious how the NTVDM works.

It seems that Microsoft bought the SoftPC solution from Insignia, a company that specialised in DOS-Emulators for UNIX-Systems. I found out that it also existed on MIPS, PPC and ALPHA Builds of Windows NT 4 which obviously don't have a V86 mode available like Intel x86 has. It turned out that Insignia shipped SoftPC with a complete emulated C-CPU which also got used by Microsoft for MIPS, PPC and ALPHA-Builds.

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As to why they didn't continue with that solution, because they didn't want to rely on SoftPC anymore or take on development themselves for a minuscule portion of users who would probably just use 32-bit Windows anyways.

Yeah. Like I said, Microsoft had the emulator. NTVDM on x64 is handled just like MIPS or Alpha, by using the SoftPC emulator. It's just a new CPU architecture.

They had a proven and tested emulator yet they chose not to build it for the new x64 CPU architecture. It turns out that it wasn't too hard to build for the new architecture either. That's the crux of my confusion.

It's not like SoftPC was new and unproven code. It doesn't feel like it would have been a major endeavor to keep supporting it.

Obviously, I don't know Microsoft's telemetry told them re: the number of 16-bit application users. I know it impacted a number of my Customers (some of whom are running DOSBox today to keep old fit-for-purpose software working) and I don't support a ton of offices or people.

It seems out of character for Microsoft to make their Customers throw away software.