FYI - I was curious so, I created an incomplete part as I was interested in only the Pad Shape and Holes.
4 Round Pads
1 Rectangular Pad, No hole
1 Square Pad, No hole
1 Square Pad, Yes hole
Only did this in the Part’s PCB svg, I was not interested in the other Part files for this test.
Did not fuss with accuracy in placing features…
Did Not fuss with Copper0/Copper1 layers, I left them as needed for all Parts I make.
Set the Rectangular and One Square Pad (both No holes) to PAD(SMD)
Set the One Square Pad (Yes hole) to a Male connector type.
Rectangular and both Square pads do not have holes in any of the Gerber files (including Drill file). Only the Round Pads have holes.
I loaded the Gerbers into CopperCam as if to CNC Mill it. Again, only the Round Pads have holes.
Rectangular and both Square Pads are SMC pads.
(including the Square Pad with Hole)
Images below… Expand the view to see full graphic