I get it, it can be super handy to share dotfiles, etc. I’ve just learned to be super paranoid about crossing the BSD and GNU streams. As long as it’s not literally blowing away files installed by the OS, then there are nonintrusive and convenient ways to keep both runtimes installed (which is mostly what this project does).
I also have dotfiles that I keep synced between Linux and Mac systems. I don’t have anything super fancy, but in the cases where the platforms differ I’ve conditionalized those parts of the scripts/dotfiles/etc. on a per-platform basis.
My likely bias here is that I am fascinated by all of the little differences between platforms and rarely want to paper over them. Similarly, I can never bring myself to use a universal remote because there’s always something lost in translation vs. the remotes it replaces (also I may have a remote control collection problem).