This is always easiest during repower. Make sure to get the pocket at the back of the engine underneath the flywheel. You just can't get that spot without removing the engine from the boat.
The engine comes back bare metal because they tank it before machining. Once it is built all you have to do is completely strip all the oil off the outside surfaces with a solvent and dry it with an air hose. Then apply paint.
All the sheetmetal is important too. The tank on the power steering pump, engine pan, pulleys and timing cover are pretty thin and will rust out quickly if not painted.
If you think this is not important price a new marine oil pan
Paint is pretty cheap, even the good stuff. Touch up is an annual for me.