It should not behave badly. You would just get less boost at higher elevations.
But will the tuning be able to deal with it successfully? That's the 'bad behavior' part I'd be worried about. If it's just less boost/power, I'll live.

Prodigy has told me that they have no plans to make their kit pass emissions inspections.
Damn. That might be the deal-breaker for me. At least the SCs are trying to get CARB compliance. Though, they've been in that state for some time now...