I got this working now - even though definitely not the intended way. ?
As I said I cannot make the settings via the UI so that they take effect. Instead I need to edit the file
~/.local/share/cura/3.3/definition_changes/<print_name>_settings.inst.cfg
which was probably the way I could have done this already.
There I can enter all settings with their respective names that I found in
resources/definitions/fdmprinter.def.json
directly. These changes are also reflected in the UI if I enable the visibility for these settings (which in turn requires the plugin to be installed).
This means the plugin is at least able to read these values if I adjust them manually in the config file. One strange exception is the setting of machine_endstop_positive_direction_z which I set to false in the config file but still is ticked in the UI. No idea why.
Still, setting this via UI would be a lot easier and preferable, so if I can help to get this working the correct way, let me know, I am glad to assist here. Also this way I have to stop Cura, change the setting in config file and start Cura again, so it would be much easier to have this changeable on the fly via UI.