Interim update:
I managed to get the propshaft off without having to remove anything more than the exhaust to gearbox mounting bracket which was a great relief. Posted it off to Proptech and got it back today, nicely turned down to 11cm diameter. The guy at Proptech said this was the third one he had done (which was little surprising since Marlin had apparantly not heard of the issue?)
I will have to wait until next weekend to check how well it fits, but it looks like it should be fine now.
Anyone ordering a propshaft from Marlin for a e30 2 litre 320i should make sure they ask for the flange to be turned down to fit.
I'll post another update when its been re-fitted which will, of course, require a test drive to confirm it works!!