Devs have to take a deeper look on Core's arg priorities.
Agreed. It seems to complicate setting up QT. As far as I know there's no settings.json for a server set up, only the GUI. It contains a notification indicating it's a dynamic file, and not something you want to edit manually. That makes it difficult and redundant if you have settings you want to control via the configuration file.
It would be nice if the common configuration modifications were available in the gui, like changing the data directory, and having a different directory for your wallets.
