Their boat their rules but I think it is a bit of over thinking the risk and the situation. If they want to have a real impact on risk and not just the appearence, it’s much more important to require masks on board and maintain social distancing as much as possible in such confined spaces, make sure captain, crew and customers are symptom free. And of course give rental gear and facilities a good cleaning between uses.
Choice of equipment and configuration should be a choice of the buddy pairs. And of course if a diver is diving (true) solo its a nonissue.