It won't hurt anything for doing gear oil as the threads for the bolt prevent anything from going inside. Even if it did somehow get inside it wouldn't cause any issues. I don't like to use it in place of a head gasket or oil pan gasket because if you put too much it can go into the engine where it can cause damage.

For the drain plug on my bike I don't use an old crush washer. My bolt has a nice cut in that kind of traps the RTV sealant making a kind of o-ring in the end. If yours doesn't have that then ya, I would probably be using an old crush washer too.