but it's irritating to perform a full row-to-column conversion through an inefficient, non-batched API in order to get the data through JDBC and into TMD

[...]

In the last two years, DuckDB improved a lot. Importantly, the C interface now provides a batched system for both inserts and querying, which enables processing very large joins

That's why. Basically JDBC doesn't offer the batched APIs needed to get the same performance.