Investigate improvements to logging for configuration

### Are there any linked Issues or Pull Requests?

- #262
- #272

### Brief description

Currently all the configuration code should be using the manual Fortran write functionality due to being called before logging is initialise (logging requires input from the config during setup). This can probably be improved with some default behaviour from the logging.

### Further details of the issue.

_No response_

Start by reading linked issues #262 and #272, then trace where configuration is processed before logging initialization. Done means agreeing on and implementing default logging behavior so configuration code no longer relies on manual Fortran writes; the issue names no files or tests.

Written by the indexing model from the issue text.