I agree that neutralizing the acid should take care of the issue, but many people use phosphoric acid as a shortcut to the work involved in abrasive prep (sanding, sandblasting, etc). No disrespect to anyone intended, but unfortunate to human nature, once we start with the easy way, it normally carries over to other areas, including the clean up methods you mentioned. In most instances where I have read discussion or recommendations on the paint and body forums for phosphoric acid treatments, rarely does anyone mention any side effects or compatibility issues. (where jomichael and sevt_chevelle got it started here, thanks!) Knowing these issues exist is the first step, as most people will get an online recommendation to use the stuff with no consideration of cross-component contamination, likely from someone not aware themselves. Unfortunately this can end up being a costly mistake after the more expensive topcoats have been applied.
If the manufacturer advises of a compatibility issue with their product and phosphoric acid, who's advice would you take? How do you insure without a doubt that all of the acid has been neutralized? Anyone at this stage should either search for a primer that does not have these side effects (if they plan to use acid...), or use a method of panel prep/rust removal (abrasion) that will not degrade any paint adhesion per the manufacturer's recommendation. As expensive as paint products are, not to mention the work involved, it pays to have all the information up front.
