Yes, the initial 64-bit OS was IA64 and that was the perfect excuse to dump NTVDM, instead of trying to do a W16OW64 or something of that sort. x64 XP and 2003 further solidified that decision because they were "professional" SKUs and Microsoft could dictate that they didn't care about DOS/Win16 for the "new" platform.
It didn't exactly run 16-bit installers. https://devblogs.microsoft.com/oldnewthing/20131031-00/?p=27...