This has all been discussed before.
The 1125 engine rights belong to Buell (though made by Rotax) and Buell isn't interested in releasing the rights to that engine. That's a dead end.
The 998cc Rotax in the Aprilia does in fact make quite a bit more HP at a very narrow peak. This is in a machine that weighs just over 1/2 of what our Spyder weighs. That engine doesn't have enough torque to get out of its own way on a Spyder. BRP already has to idle this engine up and still many (with standard clutch) have trouble getting started on a hill without killing the engine. In such situations you need liberal throttle and a fair amount of clutch slippage to go forward without stalling the engine.
Even with the modifications to get more, much needed torque out of the 998 you still have a fairly narrow power curve, (though flattened as compared to the Aprilia application).
It would have been MUCH less expensive, time consuming and easier to simply slap the Aprilia engine into the Spyder. Think of all the engineering and R&D required to come up with NEW cams, NEW port timing, injectors, etc. BRP would not have wasted their time if the Aprilia engine were a viable match for the Spyder out of the box.