Not much to add on my side but ....
I'm sure Matt mentioned this to you but we already have a fix for this and it will go out in the next update.
Just a heads up, an aligned print will never stretch or compress your print.
The first point is used to measure the XY translation of your board.
The second point is used to measure the angular rotation of your board.
If you notice your paste dispensing is consistently offset in the same direction then it implies the first point was measured wrong.
If you notice your paste is dispensing sometimes correct on some pads and wrong on other pads, then it might be your second point.
Correct me if I'm wrong @mharris, but from my understanding some pick and place systems will actually measure the location of 3 fiducials, where the 3rd point is used to measure scaling in both X and Y. Scaling issues could be in manufacturing defects in the PCB itself (unlikely), cameras playing tricks or a wonky linear system.