Be warned, this is purely speculation on my part. So far there are whispers of fueling problems (and Livernois is reportedly looking into this). Whether the stock system is literally out of capacity, or whether the ECU is throttling the system (cutting the throttle/turning off injectors, etc.) to stay within safe boundaries (prevent detonation, safeguard the transmission) has not been publicly/firmly established with repeatable logging. EBB uses a Boost-A-Pump on his Flex. 4DR Mike set up an aux fueling system to increase capacity for the HP (700+ AWHP) he was trying to achieve.
Until the system flow capacity is proven to be a problem, I'd look at the tune tables to make sure that all the i's are dotted and t's crossed for the conditions the vehicle is expected to encounter. This is a problem you run into in computer programming all the time, you have to handle all cases, however you choose to do it. Maybe in this case the full throttle scenario has not been fully tested before implementation.