Cdi...
They were very ingenious when they put this system together. In very simple terms, to hotwire a car per se, you have to supply power to the ignition then, jumper the starter solenoid. Well, with the Sea-Doo, you can jumper the starter and roll the engine over but the ignition system (CDI or DC CDI) is incorporated into the mpem.....and it's a sealed system. So, no...you'll have to get a cap programmed. But, you can do a compression test by jumping the starter solenoid to see that the pistons are good. If you get good compression and the mpem is not shot, then if there's anything wrong, it will probably not take a lot to get it going again.
Do you have a lanyard cap of any kind for a Sea-Doo? Do you know someone that does? If so, you can put a hot battery in it and put the cap on. If the electronics are good, you'll get one long beep. That will tell you that the mpem identified that as the wrong cap. That way, you'll know that the mpem is probably o.k....you may try and take a piece of wire, about 4 inches long, strip it on both ends and touch the top of the post to the metal ring around it and see what happens. I have no idea if it will cause a beep, but its worth a shot. Worse you can do is blow a fuse.