I think I've (partly) solved the mystery. I didn't mention that it's an auto trans because I assumed it wouldn't make a difference. But after digging around in your shop (the AU distributor only seems to stock the RS muffler) I note that with the Racing Beat there are differences in the exhaust between the auto and manual.
I have confirmed that my NB is definitely a 1.8, only 1.8s were sold here, according to Redbook. Anyway, I measured the dimensions between the bolt holes, they seem to be about 8.0cm, which differs a fair bit from the 8.8 listed here. So likely the reason is that I'm the first NB auto owner to buy the RS3 in Australia I guess.
I also measured the interior dimensions in of the midpipe, seems to be a shade under 4cm, so ~1.5 inches.
So it seems that in my enthusiasm I have bent the OEM bolts outwards, so they no longer accept the OEM gasket I bought. I'm thinking that my preferred solution is now, rather than drilling the exhaust again, bending the bolts, and hoping for the best, to get a replacement mid-pipe that we can be sure will be compatible with the new exhaust (and stock NB8A header).
My question is, will the 'RoadsterSport Midpipe with Catalytic Converter and Resonator, Federal Model' fit the OEM header, or am I just going to run into the same issue again?