rec: Fix sysconfdir handling in new settings code

[omoerbeek]

Short description

Partly from @RvdE, I've added the Rust side of things. It was not immediately obvious that part is needed, but there are cases where I think it is needed: running with a config-dir set to the default value on the command line should not produce a diff in YAML mode.

Fixes #13259

Checklist

I have:

• read the CONTRIBUTING.md document
• compiled this code
• tested this code
• included documentation (including possible behaviour changes)
• documented the code
• added or modified regression test(s)
• added or modified unit test(s)