A config string obtained from WiredTiger will never have duplicate top-level fields even if the config string stored in the metadata somehow does, so the thing this is checking for can't happen.

Config strings are passed through __wt_config_collapse both in alter() and when reading from `metadata:create`. This function loops through each of the fields in the base config, looks up the final value for the field from subsequent config strings, and then writes the final value. This means that the final config string will always have exactly the fields in the base config in that order, and the base config is a compile-time constant.

This check was added as a sanity check when the code was originally written, and not based on any evidence that it could actually happen even back then (in 2018).

Note that this does not apply to nested fields, so the similar check for duplicates in getApplicationMetadata() isn't dead code.