I believe so, but I haven't tested much with RSO. On my to-do list was talking to them to see if there is a better way for RSO to spawn deep sea oil by itself.
What it does now is wait for each chunk to generate, looks for crude oil spawned on water (it can spawn on both land and water), then converts all the crude oil deposits in the chunk into a single deep oil deposit. It should perform this after both vanilla and RSO have completed spawning crude oil entities.