I don't think this is a VW/Audi issue it's more of an aftermarket issue.
When I did the rear disc swap on the Mk2 the 1st set of pads I got were too thick, I couldn't put the caliper over them. I went over to the local autozone and their pads fit.
After talking to Worldpac he mentioned that they have encountered different manufactures using different thicknesses even though the backing plates are all the same. He said they've dealt with many calls of the pads not working on MK2 and MK3 applications but they fit MK4 models with no issue. He thought maybe they are making the pads MK4 spec and since the backing is the same they technically "fit" older cars.
I wouldn't put it past VW/Audi to use different compounds on different models and give them different part numbers either.