Wow. You make a great point. You got me thinking about those rainwater capture systems for downspouts now. Rainwater hits asphalt shingles and picks up a bunch of hydrocarbons, and then someone uses the contaminated water to grow their tomatoes.
Ignore the advice saying plant cells or fruiting bodies can "keep out" pollutants; this isn't true across all classes of pollutants, so best to err on the safe side.
Apart of that, is not required to wash the tomatoes directly with the grey water. Just soak the roots and the organism will take care directly of the recycling and classification of water and other stuff. Everything nasty stored in roots, stems or leaves is harmless and equivalent as cleaning it from the environment for free. Only fruits will count. Cells are good at keeping out what they don't like; and store the things that they like.
Apart from areas with heavy air pollution, rainwater as it falls from the sky is generally clean enough that it's safe to drink. Almost anywhere on the planet.
But! As soon as it hits a surface, it's easily contaminated with anything & everything: bird droppings, lead (used as an additive to zinc) from galvanized corrugated steel, etc etc.
Basically: in most places, rainwater is as clean as the collection surface / piping / storage equipment used.