If Seadoos are anything like cars, there is no difference with mechanical and hardware components these days. A 49 state and California vehicle both produce identical tailpipe emissions and have identical components. The difference is with the engine software calibration. A California emissions product has a more narrow range of normal/acceptable emissions operation. Meaning that a California vehicle has tighter tolerances and stricter range of emissions performance before turning on the check engine light for an emissions fault. A 49 state vehicle calibration will allow a wider range of emissions performance before it becomes out of spec and turns on the check engine light. The calibration could control engine operation to a small degree to maintain those tighter California standards. I didn’t know that Seadoo has 49 state and California models. Many car manufacturers still do 49 state and California emissions vehicles (which is actually now about 13 states I believe that require California emissions for cars).
I would think Seadoos follow this automotive logic, so your only risk with a California emissions Seadoo is potentially seeing the check engine light sooner and more frequently if you ever have engine combustion or fueling issues. But it shouldn’t be something to be concerned about. And no, you can’t change the engine calibration to be California or 49 state - at least on a car…it is part of the vehicle as built data that is essentially DNA of the vehicle PCM and difficult to change.