While the base TPer is highlighted right click the TPer. This will rotate the direction of the entrance. It actually worked with rotating everything in the base editor.
You have a bit to work with. Water, Docks and fish/sharks and we now a pirate Ship in the Base Builder I think. I would try for a Island Theme.
Also I bet you could use a lot of the CoT stuff for a Pirate Base.
It's not a HUGE problem so I would suggest letting it go. If it does become a HUGE problem a Mod will step in and correct it. That's what they do. It isn't a big enough problem to warrant worrying about.
I should probably let it be known I talk on the Help Channel all the time. Mostly asking for free PLs.
I have never seen a mod that does something like that. I'm pretty sure it's a more intensive fix than a texture overlay.
You can however set different Sky's in the Super Group Base editor.