IMHO the important thing is Backups. (You do backup your Library folder?)
A fresh Calibre install is easy to do. It is the rest....
Backup the (entire) Configuration folder any time you install a New plugin (name) to capture the configuration (your preferences).
Even if the PI gets updated Later, you are good as Calibre will simply notify you and your settings are not lost (notify is only for PI in the MR Index, not those other
tools)