I've got the Milltek GT 80 cat back, and I have a new standard down pipe and cat on my car both fit together
Cupra R is quite different to copra .

I see where you are coming from about flange position etc but I can't see how the 3" cobra will fit. I have one in shed to go mine and it is true 3" pipework from downpipe right to back box . Therefore I am thinking larger flange mating faces will have to have been used.

Any decent exhaust place will be able to "make" one fit but when cobra stuff is available at a decent price in the appropriate size is it worth it?

If you need any measurements off 3" cobra system let me know.;)