Not GP, but presumably it's a reference to the fact that (white) rice and (refined) pasta are processed in a way that makes them tastier but not as healthy. While you can eat brown rice and whole wheat pasta, they are quite a bit less common, and not as tasty.
Yeah, pick your poison. I've seen Prop 65 warnings on spinach, which apparently absorbs quite a bit of heavy metals from the soil. Eat your vegetables, but not too much!
"Eat cells, not substances" is a somewhat similar rule to "limit processed food intake", but the former would seem to encourage both pasta and rice while the latter would discourage pasta if you're being strict about it and rice if you're being extremely strict.