No - I would not worry. Supersprint are very very very good at getting the fit correct. Not put one on the Leon yet but had a Supersprint full system on every SEAT I have owned.
Also one of the only companies left who actually remember to gas flow all their stuff and match it to the car/engine it is intended for. If you look at the flow rates compared to other systems they are significantly better, so as you up performance they can cope to an extent. I do not work for Supersprint either.
 
After getting the price for a Supersprint system:-o I am going to go for a Magnex because I only really want the oval tailpipe.
Has anybody got one of these on a Tdi?
 
I've not see one on a Seat, but I've known other cars with Supersprint exhausts on and they have always been spot on in terms of quality and fitment.