1. You can replace the graphical shell for NT. Wikipedia even lists a few popular shells: https://en.m.wikipedia.org/wiki/List_of_alternative_shells_f...

2. NT did not begin of as a shell for DOS. You’re thinking of the other Windows desktop lineage that ended with Windows ME.

3. Even Windows 3.x and 9x (the OSs that did use DOS as a bootloader) supported alternative shells. It was literally just a one line change in a config file. I authored one such shell for Win95.