I've been using metal prep (phosphoric acid) since the early seventies with zero issues. It simply changes iron oxide (rust) to iron phosphate... which is a dead gray material that is not in an "ongoing process", like rust is. It also acts as a mild degreaser.
If you pay attention, you can actually watch the rust turn from orange to gray. If a spot is tubborn, just scotchbrite it and wet-and-wipe again with prep.
I like R-Ms 801 prep, which contains alcohol, and does not require rinsing. Just wet it good... let it sit for a moment... and wipe it away. 30-60 minutes later you can paint. ....and you aren't spending unnecessary dollars on primer and labor.
Not everything being sold is necessarily a better idea. Metal prep has been working for around a hundred years.