Likewise, TOR access is similarly configurable. Companies choose to block it because more often than not it IS bot traffic, and the few potential real customers who use TOR are deemed not worth the headaches of the rest of the network.
Cloudflare's WAF is really pretty granular, with a lot of toggles and overrides: https://developers.cloudflare.com/waf/managed-rules/
Anecdote: For small businesses with limited web resources, these are just everyday tradeoffs they have to make in order to keep hosting and security fees reasonable. At the place I worked at, previously we were spending tens of thousands a year on hosting and thousands more for a competing WAF that cost like 10x more and didn't work very well. Cloudflare let us move to a much lower hosting plan and cost like $240/yr and drastically reduced bot traffic. Not a single customer complained over the next year or two. It was a huge improvement in both performance and costs.