Overriding \Drupal\Core\Theme\Registry is dangerous because it could break many assumptions made in the theme system. Theme registry contents should be frozen but the way it's generated shouldn't. We should also be able to add features to Registry in minor releases and this isn't really possible right now because unknown places (custom/contrib/core themes and modules) trust the way it works. This logic shouldn't be overrideable (or we should tell people to not do it) because it's connected very tightly to the whole theme system.
Why this is RC eligible
This only changes documentation by marking a class internal.
Mark \Drupal\Core\Theme\Registry internal.
User interface changes
Data model changes