I have a briggs 4 stroke 5 hp air cooled. Basically, a lawnmower engine with a shaft on it. I used to take it off for the rapids, tarp the hell out of it and drybag it making sure it would stay as dry as possible. Then I would store it right side up, low in the boat and make sure it was well padded. The hope was that it would be mostly above water level if I flipped. It always started right up after the rapids.
(Skip this paragraph if you want the short of it) Then, last year the thing broke right off the steering collar mount ( damn chinese cast parts) when it got switched into reverse and went for a swim. The motor was hot and it popped cracked and made lots of steam as it died upon submersion. I yanked the thing up out of the water by the saftey strap I always put on it. I was sure we were rowing the rest of the upper section and rowing out on the "lake" but we pulled over to see what we could do anyway. The cord wouldnt pull at all so I was sure it siezed/ cracked the block when it fell in the cold water. I kept trying it and trying it, yanking and yanking, thinking if I broke the cord we would be no worse off and finally it busted loose, turned over and puked a bunch of water out of the exhaust. We kept pulling it and puking more and more water out till it stopped puking but it wouldnt start. Defeated and tired I strapped it back on the transom and we rowed on down. I would try and start it every hour or so for a few hours. Finally my girlfriend tried it and it started right up. We rigged it solidly on the transom with 6 straps and with little fine tuning of the straps along the way we had it pushing straight. We had to steer with the oars but it pushed two boats out just fine.
Now i just half ass tarp it, stick it in the boat, pad it out a little and go on down. I figure if it can get submerged and start up, a little splashing through the rapids is no big deal. Last trip it started right up after the rapids with this method of storing. I would think that drybox space would be to valuable to get wasted on a motor. I know it is on my boats.