I wouldn't argue that mixing and matching pipes/silencers would give you varied resutls (sometimes more than others) but I run an FMF pipe and put the stock silencer on for a little less noise, and the power difference, to me, is not noticeable.
Run what you can afford to run!! With FMF/pro circuit, I doubt you'd see as much of a difference as running a different silencer on a LT250r. Especially when you're talking specialized paul turner with a non-specialized fmf silencer. I wouldnt' expect to see much of a difference with your run of the mill blaster fmf/pro circuit.