Will they fit in the hole? Yes. Will the glass fit into the boot? Yes.

Other than that, they are completely different.

MK3:
no lip on the back edge of the tailgate
rear washer jet is to the left of the rear wiper arm
boot lock hole smaller
boot latch fits from the outside of the tailgate
hole on the sides to allow heated window wires to get to glass

MK4
lip on back edge of tailgate
rear washer jet is incorporated into rear wiper motor
rear wiper motor different angle to MK3 (difference is in mounting bracket built into tailgate)
boot lock hole larger and slightly recessed
boot latch fits from inside of tailgate through larger hole
no holes for wiring as MK4 screen connects @ the bottom of the screen

There may be other differences, but these are the ones which matter.

I may take the details from you though of the place making the tailgates as it may be easier to buy a good, new one than to repair an old one on my mates S1 resto.