You know what? I don't care any more. My computer is my computer. It does not need to work for other people and I don't need to work on other people's computers much. My Emacs loads many plugins, my Visual Studio is using ViEmu, I replaced my Finder and I remapped some keys on the keyboard.
This makes for a crazy confusing experience for anyone who sits down at my computer, but it works for me. And as far as compatibility is concerned, my Emacs init.el will automatically download and install all plugins it finds missing, so setting up a new computer is about as complex as copying one file.