Videocards of the era only did exclusive fullscreen - you could not for example use OpenGL to render your windowed application's UI, that was all software.
I don't think this is true? I remember successfully using OpenGL and Direct3D acceleration in windowed mode on 9x devices.
Are you thinking of the add-on 3D accelerator cards that did VGA pass-through from your 2D accelerator? It might've been true for them...
My graduation thesis was porting a particle visualisation engine from NeXTSTEP into Windows 9x.