Personally, I'd allow it, it's equivalent to the Aquam guidelines for affecting the blood in a person's body. You're affecting something you can't see, but you know to be present, with a requisite for its containing vessel.
I'd agree with you on basing this on the larger of the size modifiers for the water and the salt, but your interpretation of "Part" target would make the core rulebook's "Pit of the Gaping Earth" impossible, as you'd have to have a large enough target to affect the whole planet just to make a small pit.
The main purpose of part target seems to be to allow you to affect small pieces of things you would otherwise be unable to affect.