Paul,
Here is then response I got from Magnaflow regarding the muffler fitment, resonator constriction and construction.
MF: "The fitment of the system may be altered by the headers if it's a long tube or short tube. The muffler hanger should measure 1.6" high. I would recommend shorter aftermarket urethane isolators/bushings to get them to sit higher. The resonator in the catback system has a dual y-pipe with a single 3" core in the center."
Me: Doesn't the single 3" core inhibit performance. Is there any other alternative to using this resonator? Thanks again for your response.
MF: "The single 3" core provides better sound control and sacrifices minimal performance. The only other solution is using a dual/dual muffler which will increase flow and reduce back pressure at the expense of bottom end torque."
There's that higher backpressure = better low end torque thing.

Essentially the MF resonator is a dual Y design with each Y connected to the other via the tail end or single 3" core in the center. Speaking with Al last week, he doesn't necessarily believe that there is an inherent disadvantage here. In essence, what you have is a dual Xpipe and additional scavenging in the resonator.
I would think the constriction immediately after the collector and at the point of highest pressure and heat could affect performance more significantly than further down the line where the exhaust has begun to cool and require less volume. But I'm certainly no expert.