MDK2 wasn't idTech3 based, it was Omen (which is in more relation to Aurora)
MDK2's use of OpenGL isn't any more special. The "installer" you're referring to is the old GLSetup that usually comes with a few commercial GL games (starting with Q3 and ending around Clusterball) which was more or less an obsolete, desperate tech support method to deal with early Win9x GL ICD dilemmas more easily, and shouldn't need any installation on a Geforce2. GLSetup was originally concocted to stop a flood of "q3test dont work 3dfx" emails.
The original MDK2 retail box though is DRM'd and buggy, however... i think there's a bigger issue than MDK2 here if other games have stopped working. I know i've played it on my Geforce2 without incident almost 20 years ago, and I've never seen it fail on the newer hardware I habitually tried it on since, but I do remember the "Use DirectX for setting video modes" checkbox in the MDK2 launcher does have problems on some hardware.
by the way, DOSBox is not for running Windows 9x