Well, my opinions may not be entirely RAW, but I'll give it a shot.
I only allow one TRUE vision enhancement to run at once (Ultrasound, Thermal, Low-Light), but all the other vision enhancements (Flare Comp, Image Link, Smartlink, Vision Enhancement, Vision Mag) can run with the actual vision modes.
If you read Ultrasound, it specifically says that it over lays normal vision rather than replaces it. In 3rd edition Thermal was this way also, and I've kept that bit around. So in my games a Troll is always seeing normal vision with a Thermal overlay.