Manual installation of the plugin s repositories could be made manually once.
Then, to keep their patches persistent between upgrades, you could investigate adding their manual commands into a hook.
Some references :
- Hooks | Yunohost Documentation
- especially the post_app_upgrade one Hooks | Yunohost Documentation
- Some examples: Share your "hooks" to apply custom configurations- Partagez vos "hooks" pour appliquer des configurations personnelles
For Jellyscrub, if you cannot make it work by yourself before that, I am not sure we could help you.