Is it possible to override configuration with yml files? Override configuration guide shows how users can override configuration with global $config variable, for example by using settings.php file (the same method as for D7).

But is it possible to override the configuration in a similar way but with yml file? It's much more convenient to use yml instead of php to override settings.

A real life example: let's say my module offers some configuration but I don't want to expose it via UI. I only want users to be able to change the settings via yml files (there are reasons for that). Obviously they shouldn't change my modules yml config file. Can they create a new yml file, name it accordingly (how?) and put inside sites dir?
No, you can't override with YAML files.

But, all configuration is YAML. You can edit them manually with single export and then import again, you can do a mass export and then change the exported files (then you even get a diff of the changes that you can confirm).

You can also use drush cedit yourmodule.settings or drush cset yourmodule.settings some.key the_value (or the export/import commands for editing configuration.

None of those touch the YAML files in your module.. those are only the starting point and are then imported into the active config store of a site, after which they can be edit with the mentioned tools.