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I guess it depends on where the boat's water line is in relation to the location of the engine. If there is any part of the engine below the water line then of course you'll have lots if water gushing in there. If the manifolds are above the waterline, you can remove them safely-ish. I must say it's not very welcoming on Sea Ray's part to have to pull off manifolds to replace a starter. I suppose you have to be on your belly too, right?
You can remove the manifold while the boat is floating.