What about using thermal pads that add a bit of thickness so it will clear nearby components? Normally you want as little thermal interface material between the heatsink and the chip as possible, but since the plastic chip packages on these cards have such poor thermal conductivity, I wonder if the gains of using a larger heatsink would be worth it in the end. The card would run at a lower temperature (less stress over time) and the fan could be quieter and easy to replace.
I have some cards I could try this on at some point. Maybe I will make a project out of this... just not sure what kind of heatsinks I have on hand.
EDIT: Welp... maybe I won't do this just yet. All of the Voodoo 3 cards I have without heatsinks are also ones that have defects I haven't been able to sort out. I suspect that two of them need a reflow but I've never attempted that on a V3 and I'm not sure if I could get it to work without ruining anything.
Now for some blitting from the back buffer.