What happens if the supplied query file only uses 10 tables of 100 in a schema?

It depends on the options you pick. You can choose between a comprehensive or incremental design. If you choose comprehensive, it will supply suggested projections for all tables in a schema. If you already have projections on your tables and data loaded and are looking to get suggestions for better or query-specific projections, select incremental design. This option will then only suggest projection designs for the tables involved in the supplied queries.