Here comes the fun part: given this arrangement, I discovered that when I disembark the vehicle bay in my Seamoth the Cyclops drops it a set distance, ignoring any structures in the way. It looks a bit freaky, but it's harmless.
The odd thing is that, the way I've laid out my base, the launch bay is directly over my moonpool and almost touching it – in fact, so close that the moonpool's antenna actually pokes up through the bottom of my Cyclops and you can see it stirring around from inside the launch bay.
But you can build a base in there as I have (in my case a nuclear one, which I thought fit the ambiance) and use it to recharge any power cells that you've drained.
