Exhausts get noisier with age anyway, so it wont be as simple as "its louder than it left the factory" as in reality I suspect that a 6 month old car is louder than it left the factory if you could test it accurately enough.
Plus of course, do they actually have specific data saying what you exhaust noise would have been on the car when new that they can test it again? I suspect not.
So IMHO the bottom line is probably that they will test not against what it was as standard, but against what the noise limits were allowed to be at the time it was new.
IIRC its tested at 50cm from the tailpipe but at a 45 degree angle, where as for trackdays its normally the same distance but straight on, so I would expect the recorded value on a government test to be lower than on a trackday test, so even if your exhaust is slightly over at a trackday it may still be legal when tested slightly differently.