Yees, so the piece of software that shows/hides the boltholes on flanges checks the element type, and it only operates on FLAN and FBLI elements which would explain why @annabauman got no holes on a PCOM element.
Minor detail is there a reason why the negative geometry has a hard clash. I assume you are going to have a lot of flanges in the model is it necessary to include the negative geometry in the clash check. Adding the negative geometry will have an impact on a clash test.