It's covered under the warranty as long as the dealer doesn't accuse you of putting gas in the tank, which has happened.
There are some problems on a few cars and my best GUESS is that it's due to poor robustness of the pump due to poor fuel quality in the US combined with poor design. The pump design has been revised a few times but it could be to make it cheaper/easier to build or improve the robustness. Nobody outside of VW and Bosch knows what the pump design changes are and for what purpose. The lower quality fuel in the US vs. Europe doesn't help either. A biodiesel 2% or lubricity additive for the first few years should help protect the pump.
Then again, your 06 Jetta has camshaft and flywheel problems that most likely, every car will see. The HPFP is only a few cars. So trading one issue for another