If I understand your question correctly, the answer is to use multiple through-hole pads. Define a drill hole in each pad, assign the SAME pad number to each of the multiple pads, then position them so the drill holes fall where you want them.
If that doesn’t answer your question, can you post a datasheet, drawing, or photo that shows what you want to accomplish?
Thats what I did, I had the through hole pad and change the number to the same to the pad and after that I can route the track. Before that I didn’t know the number have to be same as the pad so I explore around and found my answer.
TlDr: the pad number is what decides which things are connected. You can have pads overlapping with different pad numbers if the symbol has the pins for both numbers and they are connected on the symbol side. (I however would consider it a hack and would advice to have overlapping pads the same number)