It would be fine. A custom tune would be best, but if its not possible a canned tune will be better than stock for sure.
I really doubt there's that big of a difference between the systems to create any long term problems. I doubt any of the canned tunes are that aggressive whereas a difference in exhaust systems would cause problems. The big thing you're doing with those canned tunes is getting rid of the emissions and noise neutering.
Woolich would be better, but there is a larger money and time expense that goes with it.
I'm using a T800 Termi tune on my bike now which has a full Akrapovic system. I had it out this last weekend and it felt amazing. I doubt I'll have my dealer load the Ducati/Akra map. I'd rather go Woolich even if it cost a bit more. Right now the bike runs so good I don't see a need though.
Same, but for my 959. The T-800 isn’t tuned to get every performance % out of the bike. It’s a safe and reliable tune, which is more important to me than another couple of ponies.