A 1 time analysis would settle the issue on a particular roof. I would put any screen at the top of the downspout where it can be cleaned easily. Those chips are a pain by themselves whether toxic or not and yes. As far as I know, I have been out of the business for a while, only the asphalt shingles have it. There may be new products out with something similar that I don't know.about. I know some codes require cedar shakes to be fireproofed with certain chemicals but have no idea if there is an adverse impact from it.
I think that if I was reroofing and was relying on roof run off to supply a cistern for drinking water, I would go with a metal roof. Since the EPA is being gutted in the U.S. and the potential for acid rain gaining ground again is strong, I would bite the bullet and buy the more expensive but more corrosion resistant copper.
