Extend INFORMATION_SCHEMA.SYSTEM_VARIABLES to show what .cnf file the value was read from. Note that included files (with !include and !includedir) should be shown, not just the master /etc/my.cnf.
Possible implementation, load_defaults() adds (may be on request only) special options in the argv list, like --file-name /my/cnf/path. And handle_options() uses that (comparing pointers, just like with --separator--).
This could go into GLOBAL_VALUE_ORIGIN column or into a new column, say, GLOBAL_VALUE_ORIGIN_INFO
which would have a file name for CONFIG, and, say, username for SQL.
It's really difficult to check that MySQL/MariaDB is using my.cnf or not. Also we can't check that what are the default values of variables through mysql client. It would be really helpful if we can do like
1. Add 3rd column like "last updated by" (read cnf, set global, set session, default)
2. Make separate command like SHOW DEFAULT VARIABLES
3. Adding columns to information_schema.global_variables to check details