Having worked on several ISP networks that practice isn’t nearly as common as many people seam to think. It would be technically difficult to do that at the rate of a large ISP.
There could be capacity issues between an ISP and some content providers but that is different than throttling or optimizing traffic.
The fast.com speedtest is run by Netflix, for presumably this same reason.
I thought it was pretty well known at this point that ISPs optimize traffic for speed-test sites and throttle a lot of regular traffic, especially during heavy-traffic times like the after-dinner Netflix bump. Since this is a new tool, a plausible explanation for lower speeds is that not all of the ISPs' network engineers have had a chance to prioritize Cloudflare's speed test traffic on their routers along with the other speed test tools.
Part of me wonders if this is part of a ploy by Cloudflare to avoid throttling by ISPs. If they design it right, the ISP can't tell the difference beween the speed test and regular CDN content, which would be extremely clever.