For a large repository it could take many days (10's or 100's? of days) to rebuild the indexes from scratch. Since queries all return no results when the indexes are missing it is probable that you don't want a system in production to startup if the indexes are missing. You probably want to find out why they are missing before doing anything else. Rebuilding from scratch is a very last option.

So, a startup option to cause the repository initialisation to fail if the indexes are missing would be useful.