Well, I went for a ride today, I took my 96GSX, which has a 787 not a 717. I didn't notice and difference in the temperature of the engine and the temperature of the mag. covdr. The cover might have been slightly warmer but you could comfortably put your hand on the engine as well as the magneto cover. I didn't have an infrared temp. gun but they were both just warm to the touch.
The rotax engine is not over heated unless the temp. reaches over 200 degrees F so if the alarm is not sounding I wouldn't worry about it.
Like Strizzo I have no idea why your magneto cover is getting hot, I would also suggest that you remove the cover and take a look. This is not a problem that I have ever had or ever heard of. If you choose not to follow our advice you should just take it to a dealer and have them check it out.
Lou