All ultimates scale off max resource and the crit value of that resource. Example being dawnbreaker. Even though it's phyiscal damage, if used on a magicka class it still scales based on your max magicka and spell crit. Same for the other way round, if using meteor, although it's dealing flame/ice damage if used on a stamina build it's scaling off your max stam and weapon crit.
However, does it also scale off of your spell/weapon penetration too (dawnbreaker would scale off your spell pen if used on a magicka build, or weapon pen if used on a stamina build for example)?