drill hole in protel
The holes in the PCB are defined by pads. You can't have a hole without defining a pad. Wherever you place a thru-hole pad on the PCB, a drill is defined by the size of the hole assignment in the pad.
The location and size of those holes in the pads are used when generating the NC Drill files, and by the ".Legend" string on the Drill Drawing layer to generate a drill table.
The fab is only interested in the NC drill files. The Drill Drawing, and drill table, are just there to provide a visual confirmation check - not for actually drilling the board. The NC drill file is the one they load into their multi-head drilling machine.