This should not be happening. You should be able to prioritize your list of toons and have them stay where you want them too. I believe this information is kept locally on your computer. For some reason it sounds like it isn't being written or retrieved when you exit or enter the game.
Some Costume options are Male or Female only. The Japanese Pants are an older costume option so it may have been a decision made by the Devs ages ago to make them Male only.
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.