Okay, but why not just do that to solve your original issue?
Because, I think, this could be beneficial to everybody, not just me. Moreover, there is possibly some details to consider, before going that way. Out of experience, keeping data, applications, libraries and configuration separated, avoid mistakes like removing important data or configuration while removing/upgrading an application. I do expect the game to reach some stability in terms of data file format, so the need to play multiple version should fade away at some point. I play only the last version available, as I don't see a need to play with older versions.
Now that I know the directories can be specified in the starsector.sh script, I will see what can be done to suit my needs.
It's rather funny the thread says "each platform", but discussion is only about Linux.
I play on Windows and I prefer the way the game works now. I don't have to guess where stuff is and I can keep multiple versions, if I have to.
Linux is the sole platform I know enough to detail how data and applications should be organized. This is why I talk about the linux platform, essentially. However, starsector is available on other OSes, so those OSes should be part of the suggestion, too.