As the config file read order defined by the order of the lists at https://github.com/python/mypy/blob/master/mypy/defaults.py#L15
is

CONFIG_FILES = CONFIG_FILE + SHARED_CONFIG_FILES + USER_CONFIG_FILES  # type: Final

a shared config file (which may exist for several other purposes) shadows any user config files even in the case when
the shared config file contains no mypy section.

Steps to reproduce:

• Create an empty setup.cfg in the current directory, and also have one of the USER_CONFIG_FILE versions of a mypy config file.
• Run mypy
• Notice that only the setup.cfg file was read, even though it had no mypy section.
  `

Proposal

The logic which checks for a mypy section in the parser object (https://github.com/python/mypy/blob/master/mypy/config_parser.py#L127) should be used to check whether the parser.read call actually loaded anything meaningful from the config file. If no mypy section was loaded, then the loop over the config_files should continue instead of breaking.

This should at least be the case for any shared config files which may exist for entirely other reasons.