Here is my temporary solution:
- Create an empty vault on my laptop and set the configuration folder to .obsidian-mobile. Then configure the vault how I want the mobile vault to be configured and set this empty vault to synch and synch settings.
- In the mobile app set it to .obsidian-mobile and set it to sync settings.
This seems to have worked and the updated settings on the laptop synced to the mobile app. However it is a complicated workaround. There should be ways to completely manage a configuration with css snippets on mobile without have to create settings outside the mobile app, use other apps, etc.