I’ve been looking into version compatibility with renpy and it seems one can put RenPy 6.99 as a drop in replacement for the prebuilt one. This is how https://github.com/flathub/com.katawa_s ... tawaShoujo and https://aur.archlinux.org/packages/katawa-shoujo/ work. They don’t modify the game itself (they just download it from the site) a side effect of doing this is a bunch of minor bugs are fixed. One example is full screen will not stretch and keep its aspect ratio.
Also, to be clear, this is not modifying the game in any way. All this is doing is launching the game with an updated version of RenPy. The way it works, is just by calling renpy to the game folder of KS.