Pretty much any of the tuneable aftermarket ECU's should be able to handle boost. I know the Megasquirt and AEM (what Mopar sells) can handle boost. Not sure on the FAST XFI setup (the EZ EFI I know can't), but I would imagine it can probably handle it since it's a higher end system. It mainly just boils down to whether it can read a 2+ bar MAP sensor.
Along those lines I think pretty much every other aftermarket system also uses a cable throttle body. Not sure I've ever heard of one actually using the stocker as of yet. I believe the FAST kit comes with a new one as part of it (I believe it's actually a GM piece with an adapter, correct me if I'm wrong). Mopar sells one for their kit as well I believe (must be made of platinum though for the price they want). The Megasquirt may be able to use the stock pedal if someone wants to have fun with wiring and circuits to control it, but safety is always an issue there and most just prefer to swap to a cable.