ALL new mufflers and exhaust systems will change in sound a bit after they "break in", they heat up and cool down a few times, and they get a "coating" on the inside of the pipes.
Flowmaster ABSOLUTLY get a bit louder than when they were first installed. It has nothing to do that they use baffles. I've installed Flowmasters on EVERY gas truck I've ever owned, they ALL get louder. Also my Buddy's have had more Mustangs that I can remember. One time, my Cousin got a 98 Cobra and got a Flowmaster system installed, and he was VERY unhappy with the way it sounded (too quiet), but I told him to wait a week or so, then it came to life and he loves it!!
One note, they should only get louder to a point, they shouldn't keep getting louder and louder.
As for reliability, Flowmasters are aluminized, and should outlast your X (outlasting an X shouldn't be that hard), BUT only 1 time did I see a Flowmaster completly rust, on a guys 91 Camaro, he parked the car in the middle of the winter and it sat for a year with road salt still underneth, when he wanted to get the car running, again, we put it on a lift and the WHOLE underside was rusted, even the aluminized Flowmaster.