I think it depends on what your goals are as to which what car to get. If you want 300-350 flywheel hp either of the cars will get you there easily. If you want to make big power get the 05-10 GT. The V6 aftermarket will never offer the sheer amount of parts that will be available for the 4.6 3V engine.
If you get an 05-07 GT it wont have a warranty to ruin so mod away. I dont think I could throw a blower on a brand new car until after the 3rd year. Its one of the reason I did not get a 11GT. You kill the warranty and blow the engine it will be BIG bucks to get it fixed. I saw a 4.6 3V brand new shortblock for under $2K and for $3-5K you can get a forged offering that will swallow all the boost you can give it.
My other option was a 11 GT500 with a FRPP blower installed on delivery with complete warranty. That would of been the BEST deal ever. Too bad it would of been a $60K+ deal adn I cant justify that much coin for a car right now.
2005 Ford Mustang GT Torch Red Manual
Saleen Super Shaker 3.4 pulley/Brenspeed Tune
Kooks Longtubes Catted H/FRPP Stingers
Full BMR And Steeda Suspension
SOLD!! I have no Mustang at this time!