Problem

Due to technical limitations API Tokens can't be used for authentication on the Confluence remote API (XML-RPC & SOAP).
Atlassian has deprecated the RPC endpoint since Confluence 5.5 already, read here for more details.
Sadly, not all methods of that API have been replaced by REST methods, i.e. a REST API methods to administer space permissions.

Workaround

Since you can only use passwords for the RPC API, here is what you could do:

• create/ use a dedicated account for your RPC automation and set a strong password for it

• navigate to the System-Wide settings configuration page in the API Token app
  

  

• scroll to the Password Authentication section and make sure that Allow Basic Authentication with User Password on the Confluence Remote API (XML-RPC & SOAP) is checked:
  
  

  

Of course you only need to check that option, if Disable Basic Authentication with User Password  is also selected,
which is usually the case, if you want to prevent that users can also use regular passwords for authentication on the REST API.
With both options enabled like that, our app won't block authentication requests with passwords on the RPC endpoint but still will for all the other endpoints.