The menu_link_content entity has only one bundle in drupal core (with the same name as the entity).
During the development cycle before Drupal 8 stable there was an implementation for bundles with this entity but it ended up having one single bundle just like the user entity.
So the idea is that menu_link_content shouldn't be different than user at having a single bundle to play nice with field_ui and also be a good example for other single bundle entities. In the current situation we kind of half-care for contrib modules that might want to implement bundles since they can add the bundle key themselves but also force them to override the entity class to get somehow override the preCreate() method on the current class entity.