Yes, it does. TuneECU allows disabling SAI, but I am not convinced that it actually functions as intended on the new Rocket. We know already that TuneECU cannot raise the rev limit above 7000 rpm - not on mine anyway - and that it cannot clear all engine errors even if it reports the contrary.
Penner's tune has tamed the decel pop to a pleasant gargle, which I prefer to the absence of any. It suits the beast IMHO (-:
Here is a DynoJet FAQ discussion, confirming your experience adding fuel;
Deceleration popping in the exhaust. This can be done incrementally, using TuneECU but would be best attempted during a dyno tune unless one wishes to load multiple tune iterations by thumbsucking values and range.