I'd think that the Updater plugin is intended to update the one jEdit installation and configuration the Updater has been launched from.
So, the Updater plugin should ask the installer to:
- use the given jEdit settings directory
- use the given jEdit Home (resp. program) directory
- don't let the user change these directories
(See related request for installer #2878349)
What does it mean for the installer to use the given settings directory?
The startup script is what determines / overrides the settings directory and updater just needs the location of the startup script.
The jEdit home directory is the default value that is already used for Updater's options, so the user does not need to set it.
the "installation directory" seems totally unnecessary as a user-configurable text field in those options however, so it might make sense to remove it?