Here's another suggestion. When there are upgrades and we reach the step where we want to choose which modules to install, it would also be user friendly to have the modules already installed auto selected so that the user understands which modules they have installed already.
The problem with the existing user flow is that since there are so many modules, the user has to remember which modules they've installed. So if the modules that are already installed were preselected, it would make the process of upgrading easier.