I can't say who's right or wrong, I haven't tried either method yet (and you're crazy if you think I'm paying for a jet kit ;P). What I do know is that FOG has the most seat/dyno/race time on these bikes. The only real way to solve any of it would be with dyno sheets and time slips and it's not worth fighting about as bench-racers.
But on top of everything I'm going with results. 9 out of 10 people that have talked about installing their exhaust have just tuned the pilots and been golden. No jet changes, no shims, just pop out the caps and grab a screwdriver. Honestly, I'd try that first, you don't even have to take the carbs off and if everything runs well afterward then you're done. Just put the exhaust on and try it out, you're not going to kill the bike with a short test ride and evaluation. Most likely you'll get some popping on decel, which can be ignored if you don't mind it (my bike's done it since I "fixed" the exhaust. If you get a flat spot (around 6000 to 8000 rpms) then you need to hit the pilots. If tuning the pilots doesn't work, then you don't have a choice but to pull the carbs and swap the jets.
But on top of everything I'm going with results. 9 out of 10 people that have talked about installing their exhaust have just tuned the pilots and been golden. No jet changes, no shims, just pop out the caps and grab a screwdriver. Honestly, I'd try that first, you don't even have to take the carbs off and if everything runs well afterward then you're done. Just put the exhaust on and try it out, you're not going to kill the bike with a short test ride and evaluation. Most likely you'll get some popping on decel, which can be ignored if you don't mind it (my bike's done it since I "fixed" the exhaust. If you get a flat spot (around 6000 to 8000 rpms) then you need to hit the pilots. If tuning the pilots doesn't work, then you don't have a choice but to pull the carbs and swap the jets.