The acid treatment is temperamental. It won’t work fully if the metal is somewhat clean. It reacts with iron oxide (rust) to form the iron phosphate. So if you apply it to somewhat clean cast iron, you’ll have untreated spots that will rust. You’ll see them—those areas won’t turn black, or just barely so.
What I do? If I’m going to leave it bare, I’ll actually spray it with water and let it flash rust, then treat with acid. If I’m going to paint, I get it as clean as possible, treat, flush with plenty of water, then paint—preferably with epoxy paint.
For a water jacket, I’d use method one. Blast the jackets out, let them air dry fully, they should flash rust. Then acid treat. Let that dry, flush again with plenty of water. That should be more than enough protection, especially with anti-corrosives in fresh antifreeze.