The braking issue seems limited to the base GT brakes, which is the same brake on the 2.3 EB PP. I've not seen anyone report a resolution yet. I have the 15" Brembo on a GT PP, no noises.
I've not seen a Tune available from Ford Racing for the 2015 Mustang, yet. While a Tune will not void your vehicle warranty, any warranty related issues to a Tune could have them blaming the Tune and deny said warranty claim.
Because it really isn't needed since the stock torque converter is limited to how many RPM's it can flash to. This is not a Ford design limitation, but a torque converter design limitation. If you want to drag race with a automatic and want a higher rpm flash to launch off the line with, you have to get something like a Circle D high stall converter. The down side to this is that driving at normal low rpm cruising speeds will take more throttle to move the car the same since the converter will essentially be like a constantly slipping clutch until the converters designed rpm range is reached.