OK, got the car leveled (yes leveled!) up on jack stands and checked a few other places for reference, for all the paranoid, detail oriented, even anal people out there that like to do things right, everyone else can just suck it.
Pinch weld, Rocker panel and Threshold are all pretty much on the same plane, so checking any of those spots will work, it's just the threshold is more convenient.
Transmission case is definitely not level, it's exactly like the cutaway view of the drive line shows, about a 5 degree decline. Bottom side of the pan is much closer to level but it still angles about 1.5 degrees toward the rear, which make sense since the main drain plug is at the rear of the pan.