The intercooler draining as described in the manual is for the AIR portion of the unit to clear any water condensation in the AIR portion, where you remove the AIR outlet hose then start and rev the engine up to 4000 rpm several times. Just make sure you don't run the engine for more than 2 minutes (I did it all in about 30 seconds), and always run it with fresh water going into the flushing port as described in the exhaust system flushing section in the manual. I have done this procedure twice already as this is my second winter with the 165 ID. Nothing came out of the intercooler. If you don't do it, it probably won't hurt your boat. It there was any water condensation, it's most likely not enough to cause damage in freezing conditions.
As for exhaust system and Intercooler protection, I used the compressed air method as described in the Rotax manual last year without any problem. Same thing this year (I am in New Hampshire btw). Antifreeze is cheap, but air is free. It's much quicker, simpler, and cleaner. Most importantly, it is environmentally friendly. Like used motor oil, you cannot dump antifreeze anywhere. It must be taken to a recycling center. FYI, last year, my boat was on the trailer on a slightly inclined slope, only about 1/2 cup of water came out. This year, the boat is on a cradle horizontally with and above the water, 2-3 cups of water came out. Undoubtedly, there is still water in the system but not enough to cause any damage. This is what the engine manufacturer wants you to do, not the antifreeze method.