Hey! Thanks for the tips, and for tinkering with and enjoying the game!
The save files and some of the general data structures are still WIP and being constantly reworked from previous versions, though that's currently a very low priority when compared to working on new features.
It's still very little impact on file sizes, and it's almost guaranteed the game will change enough from version to version that it'll break the older saves entirely, so at the moment I'm not paying too much attention to how the files are structured!