It's the Voodoo's Voltage Regulator making the Heat Arnljot. Put the active cooling on the Regulator & leave the Voodoo heatsink passive, or actively cool both for enhanced cooling.

If there was any concern @ the difference of 3.3v or 5v on the PCI side of things when using a Voodoo, the Voodoo wouldn't work & you'd either kill the Voodoo for over volting or it wouldn't work for not enough volting. Don't concern yourself with PCI voltages RE PCI Graphic card solutions on Mediators or G-REX's. Just make sure you have the right Radeon model or the right Voodoo model & be sure to set up the G-REX drivers with the correct parameters during the installation process.
Also, make sure your Edge connector off the PPC card is really snug into the G-REX backplane connector. It's best to assemble the PPC card & the G-REX connections first whilst out of the mainboard on the workbench & very carefully align the ZORRO connector & CPU connector whilst gently nudging the whole assembly in place. You should also be using the Processor Card Mobo Stand offs on the G-REX side, so extra care is needed to align these at the same time.
Kin