MattZ28- There shouldn't be a problem claying frequently as long as you do it gently. I've been spot-claying my vehicles at almost every wash for years, no problems. But aggressive claying (to remove rust spots) might be a different story. Still, letting the rust go wouldn't be good either!
Using the 3-step stuff all the time would *NOT* be a good idea, but the point is that the acidic step is supposed to burn out all the rust- it shouldn't come back. And this is why this method is preferable to claying. Clay doesn't always remove *all* of the ferrous contaminants so the rust keeps coming back.
I dunno about polishing the spots away...much as I love the 1Z PP, that's not how I'd approach this. I'd at least clay them until they appear to be gone (I know you tried, but still, I'd try it again).
Hard to say if something was in the paint before the Zaino or if the Zaino wore away and something got in there then :nixweiss Either way, I'd think the problem is the same, unless there are ferrous contaminants *under* the repaint, in which case your friend has real trouble in store.
As far as preventing them (new ones), just claying while such contamination is just in the LSP (you clay stuff out of the LSP, so gently that you don't *remove* the LSP), before it affects the paint itself, and keeping the LSP refreshed works for me. My silver vehicles really show those rust spots too, and this method is the best I've come up with.