You're right, not 100%, but very close if your mods are of a similar spec to those the tune was designed for, and if I guessed with fuelling, TTP wouldn't exist!
No, I haven't tested every pipe and other mod out there, but I do have a store room full of silencers including the most popular ones and I have tested the configurations TTP tunes were designed for. When you spend hundreds of hours on the dyno and road testing, you very soon realise that the biggest change in fuelling for free flowing silencers is dictated by the length of silencer used. For TTP tunes to stay as close as possible to that 100%, there are tunes for both long and short free flowing silencers.
I have a lot to lose if I get it wrong and TTP is in existence to make a buck from the twins, but I can assure you it is not a quick one and is based on good solid testing, customer service and fact.
"Keep a open mind my friend and you will keep on learning." That sounds pretty God like.