The version of Atom used by RenPy is locked at 1.35.0 (or 1.35.1). It comes pre-installed with the packages that RenPy needs and a preset configuration (including syntax highlighting). I believe it's using the "portable" edition, which won't auto-update. In fact, trying to run Atom 1.37.+ breaks some of the functionality that we take for granted (Loading the list of files within the same project without opening it explicitly as a project). So even though the latest version is 1.60.0?, RenPy is still using 1.35.0.
In theory, PyTom doesn't need to do anything - since it will continue to work as it has done since March 2019 - which was the last time RenPy updated it. The RenPy installer doesn't grab it from atom.io's site either.
The only restriction I can see is if you use additional packages not already shipped with RenPy (for example, I use minimap).
I guess we'll just need to be careful with our backups.