I am going to make a post soon, especially if people are interested, about how to use Boxbuddy with Distrobox to create mutable atomized linux distributions you can add packages to and do whatever you want with while retaining the vanilla immutable Vanilla SteamOS settings.

I am still encountering some limitations but I have Debian with R and Python along with multiple geospatial packages for both languages and Pandoc installed in an atomized linux distribution and it works great. I just installed emacs on the atomized linux distribution itself and having been using org mode to execute R and Python with codeblocks and set up a workflow that way.