The new mazda's are crazy sensitive to any type of changes whatsoever. They have redundant sensors which check and balance each other. If things are just off a little bit, the car starts throwing codes. A short trip down the road with the cutoff enabled probably won't be enough to throw a cel, but a trip or two down the track might.
The main restriction in the MPS 6 exhaust is the section after the turbo, prior to the main cat. This is the section which the aftermarket community is working on tuning for maximum power gains.
The main cat shouldn't be a major restriction, as its #2 in the restriction formula. You always have to start at the source, then work your way out if you want max power gains.
http://forum.mazda6tech.com/viewtopic.php?t=4210
Note the giant stupid precat right after the friggin turbo, then a stupid bend, another bend, then it feeds right into a nice straight pipe with a nicely sized cat. The WU-TWC and Front Pipe section are going to be your power adders.
One thing the cutoff websites fail to mention is the effect of adding a cutoff system to an exhaust when the cutoff is closed off. It creates turbulence and interrupts the smooth flow of exhaust out the rear of the car. Huh? What? Ya thats right, you reduce your power output when its closed. It acts as a sort of restriction to the smooth flow of the exhaust.