From reading dvc/config.py I see that configpath option of S3 configuration is not included into Config._map_dirs(). This will mean that any relative paths there would be resolved concerning current dir not the dir config file is in.

So the fix is to include configpath into Config._map_dirs().

The more complex fix, which will save from future errors of this type is removing duplication. I.e. using some subtype of str, in dvc/config_schema.py to mark things to be handled specially. Deducing schema in Config._map_dirs() automatically.