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Yes it does. As skydog said, the increase in articulation takes away any of the already small margin of error that modern kevlar head snares allow. With the top snare on you can hear EVERYTHING. Some lines cut the (bottom) guts off of the outside snares in order to "tune them out," and make the line sound cleaner. Adding the top snare is the opposite effect. Any dirt that's present is magnified.
Let me elaborate a little bit on my view on this:
I agree with you on the MTS unit making the sound more articulate. The pressure that's put on the top head by the MTS system cranks up the pitch of the top head, making the sound higher and shorter yet still wet. That's the beauty of this system and the down fall at the same time.
If the line is at high calibur, the MTS unit does not matter. Whether the unit is on or not, there is only one way to play "clean". There is only one way to play correctly in Tempo and there is only one way a line of 7-10 snare drummers will all play correct at the same time.
The difficult thing is, it's rather rare to see any drumline that can play that accurately, even in drum corps level. Therefore, even without the MTS system, snarelines need to cut out few guts because playing in a line of 7-10 drummers with all the gut response makes the sound extremely thick, even if their playing something close to clean. However, in retrospect, if all but one snare guts were taken out, the only thing we would hear is the impact of the stick on the top head with a very thin snare response. This would make the flaws very apparent. What the MTS does is similar to this: making the sound shorter and articulate. Playing with a very articulate sound will only make the dirt more apparent. So yes, it'll require much attention to make it sound clean and perfect, but it'll be easier to spot dirt.
If any one would recall, SCV has kept all their guts until the staff change in 06. 04 and 03 was amazingly clean, yet they still kept all their guts. I believe, if they had the MTS system on their snare turned on the whole time they would still sound just as amazing.
Bottomline, I think we just had a different definition of what "clean" is.
I hope that clear things up.
-Scott