I used the factory guide holes when I put the subframe back on but later decided to use the factory alignment measurements in the Service Manual. Glad I did - using the guide holes is a rough approximation in my opinion. The most important measurement is the cross one from the rear corner of the subframe to the opposite rear frame rail.
When I did it the 2nd time, I had did not have any of the front clip on and would think you could be shifting enough to cause front clip sheetmetal to kiss the doors or something else.
