Perhaps the muffler and filter mod added midrange power not peak power, everyone quotes peak power but racing with a stock trans your not always sitting at peak power so midrange power gains are usually more benificial.
I agree adding better flowing filter and muffler is benifical, engine is an air pump, allow the air in and out with less restriction and the air pump is more efficient, more efficient = less power lost to pumping restriction = more power to the flywheel.
Even if the turbo is the largest restriction in the exhaust, a better flowing muffler is still going to help because of the pressure differential between the hot side pipe compared to downpipe, also free-er flowing post turbo will reduce backpressure and keep EGT's down, which can lead to a colder denser intake charge which will lean out the Air/Fuel ratio which will also make more power...
My dad said the same thing to me about an internal combustion engine when I was a kid and didn't forget it lol. Faster air goes in and out, the better. I agree with everything you have said.