The intrusiveness of the registry in terms of database configuration depends on which RDBMS you're using.
I use it with PostgreSQL and I don't use a separate database for the registry. I do have a separate schema for the registry in the same database as the data, but I would want that sort of organization no matter the case. If the database you use doesn't include some sense of "schema" below the database level of separation, I could see how that would be annoying from an administrative/maintenance point of view (or on hosted database solutions).
I use it with PostgreSQL and I don't use a separate database for the registry. I do have a separate schema for the registry in the same database as the data, but I would want that sort of organization no matter the case. If the database you use doesn't include some sense of "schema" below the database level of separation, I could see how that would be annoying from an administrative/maintenance point of view (or on hosted database solutions).