Is it possible to override configuration with yml files?
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.