At the time Windows 95/98/Me lacked certain features so it's possible they wanted to experiment with things like multi-threading/processing. NT also supported Intel's physical address extensions, PAE, to address 64GB of RAM using an extra 4 bits of memory address creating 16x 4GB banks. Might have helped them in the development phase as map compiling took a lot of resources back then. Its also possible they saw that NT was the future of Windows as Win 2k married the multimedia stack of Win 9x with the more capable NT kernel. That led to XP which finally killed the Win 9x family.

I tried running Quake 2 on Windows NT 4 before 2k came out so like '98/'99 but had an issue as NT lacked DirectX. My memory has faded and I don't remember if the installer failed or it failed to run. I think it was the former as I have a recollection of something complaining about missing DirectX.

I do know that multi-processing was implemented in Quake 3 and I specifically ran Windows 2000 for that.

Why not? id was always into cross platform support, quake had a linux and solaris port weeks after launch, and mac a year later or so.

Probably at least in part for the same reason they used NextStep, because it wasn't prone to taking down the entire OS due to stray pointer dereferences during development, as was possible with Win95.