Disabling missing modules results in a "Unable to install MODULE already exists in active configuration" warning or PreExistingConfigException (via Drush)

Problem/Motivation

update_fix_compatibility() is just remove modules and themes that don't exist.

Steps to replicate

1. delete a module from the modules folder
2. run updates
3. restore the module and try to enable it

You can't enable nor uninstall. But it does point to the process of disabling the module leaving things in a corrupt state.

Proposed resolution

Remaining tasks

User interface changes

API changes

Data model changes

Release notes snippet