Hi Jakub,
The Material class has a member called bAutomaticallySetUsageInEditor which allows for the usage flags to be updated automatically. Look for it under the Usage\Advanced section in the material editor. The default value for that attribute when creating a new material is decided through the project settings. Look for Rendering\Materials\Automatically set Material usage flags in editor default
The engine default is to automatically set the usage flags for accessibility reasons. Lots of advanced users to turn this off.
Regards,
Martin