GPU install screw holes not aligned

Finished steps to remove GPU assembly per repair guide. Tried to install replacement GPU assembly and the holes on the GPU board do not align with the holes on the logic board, they are slightly off, the screw will not be able to go in perpendicular. I confirmed I'm putting the GPU pins into the upper half of the black receptacle on the logic board, the u-shaped divider channel looks aligned, I'm putting what I think is adequate pressure. Comparing what I see versus the repair guide photo, mine seems like the GPU assembly is not as far in as the photos. I move the replacement assembly aside, and tried to put the original assembly in, and it also doesn't align with the holes. So I must be doing something wrong, I just can't figure out what I'm doing wrong. The hole at the heat sink aligns ok.