The "rules" for config are different. Code, test code, and config are different, their complexity scales in different ways of course.

By way of analogy for why the two configs are different, for example Two beaches are not the same because they both have very similar sand.

You really have two different configs.. You also have one set of configs. You didn't set up an application that also fetches some config that is already provided. It would be like having a test flag in both config and database, sane flag - two places.

Where config duplication goes bad is when repeatedly the same change is made across all N, local variations have to be reconciled each time and it is N sets of testing you need to do. Something like that in code is potentially more complex, more obviously a duplication of a module, just more likely to be a problem overall.