I agree there are tonal differences, but I wouldn't say "don't even think about it". They're made for the cash-strapped players wanting to play PRS guitars, in which they can then upgrade it with USA parts down the road. The SEs made many people's dreams to come true (including me). Plus, with all those artists playing stock SE signatures instead of USA PRS, I doubt that they hear huge tonal differences.
I have changed everything within my SE guitar from pots, locking tuners, pickups, input jack and selector switch. I had to have the frets leveled as well. $700+ later the guitar doesn't sound much different than it did prior to the modifications. All done by a Luthier. The tonal differences are huge. I had everything but the wood converted over to USA parts. When you play the SE next to my custom 22 there is no comparison.