Yes, the JL uses throttle-by-wire... this is where products like you mentioned (pedal commander, pulsar, etc) come into play... they are manipulating the "signal" between the pedal and the ecu...is it possibly the drive by wire? That is typically the cause for laggy throttle response on new vehicles these days.
What I am wondering is, do tuners have any ability to alter the ecu in a way that would simulate what those products are doing to eliminate the need to use both?
But I think I need to stop asking questions and just get my #%$! forced induction installed and see for myself