The SQL layer (which is compared to Google F1 in the blog post) is open-source (it is not yet released; an older version is on GitHub: https://github.com/FoundationDB/sql-layer). This means that the SQL parser, query planner, execution engine, etc. can all be audited, examined, and changed.

You are correct that the FoundationDB storage engine itself (transactional key-value store) is closed-source. (It is free for production use in smaller cluster, and available for license for larger clusters.)