What I mean by "direct database query" is the use of low-level functions to retrieve posts or terms from the database, rather than WP_Query(), get_posts(), get_pages(), get_terms(), etc. To impose content-specific restrictions and roles, Role Scoper must append conditional clauses to your query. The problems that arise are:

a) if you use $wpdb->get_results(), Role Scoper can filter the query, but must guess at the nature and context of the query by looking at a lot of variables that are not necessarily fully descriptive or forward compatible, including the query itself.

b) if you use the mysql functions, Role Scoper cannot filter the query at all

If another plugin uses the mysql_query() function directly, Role Scoper will not modify the query or result set at all. So yes, it is a "passthrough" situation. The issue is not about data being discarded.