That's correct, they moved up, sorry I didn't make that clearer.
Bottom line, do whatever you can to get the car in a stable position before cutting and during the assembly. It may work the other way but why risk it?
I put the rear assy in the vehicle and sat the axle tubes on two jack stands close to the flanges to load the chassis. That way the tires were not in the way of fitting and welding the wheel well area of the qtr. Maybe overkill but it turned out nice.