My boat is in warm saltwater all season. The Yamaha manual specifies storing in the water in the down position, (not specifying why) and flushing in the up position with built in hose connection...not muffs...with the engine off (supply tubing is too small to cool properly with engine on). I speculate it's concern that in the up position the rear cowling air intake points straight up, and in a very heavy rain (we got 6 inches in one hour in April) it could overwhelm the air separator and send water down into the engine air intake, which would not be a good thing. I asked my 5 star Yamaha service chief and he says 'I keep mine up.' Looking around the marinas every Sea Tow and commercial boat has them up. I flush after every outing, keep a waterproof fabric engine cover on it on return, so no water can get down the air intake. I run the rams all the way down so they're not exposed (Dr Bob's idea), which leaves 3 square inches of skeg in the water. I replaced the Guest galvanic isolator with a fail-safe Pro-Mariner and check with a Marinco GalvanAlert monthly. Every 3 months I pull her out and have Accu-Prop fix any dings, replace the engine transom bracket anodes (which are always under water and collect growth that's too dense to wire brush off for $40), clean up the skeg, brush off the slime line, Hydrocoat the drain plugs and Tuff-gel the brass plugs in the aluminum engine bracket, and swipe on a couple coats of Poli-Glow in the high-wear areas. Down here, you can't wax in the sun, and you can't wax in the rain, so you can't wax at all between April and November. No more waxing ever again. Now that Poli-Glow has an aerosol stripper it's easy to remove. ( I acknowledge I'm an outlier fan here, but I loved the stuff on the Regal 2665 in years 5 through 9 too after lots of UV oxidation gelcoat damage. Count on several days de-waxing, wet-sanding initial prep). Fill up with 150g of ethanol-free gas + Yamaha Ring Free + Star-Tron and we're good for the rest of the season. Compared to re-building and flying antique jet aircraft, this hobby is cheap.
Bottom line, I ignore the manual, trust my service guy, mitigate against rain/hose water ingestion, and see ALL the other owners of all engine brands in the 8-350 hp range doing it the same way. Your mileage WILL differ.
Cheers!
John