As far as I know, Cloudflare transparently redirects some Tor users to their own hidden services and then uses the circuit ID for rate limiting: https://blog.cloudflare.com/cloudflare-onion-service/

"Some" because they seem to have internal heuristics for detecting Tor Browser users before they enable that feature for a connection, so it doesn't apply to all connections made through Tor. YMMV I guess but I haven't seen a Cloudflare CAPTCHA over Tor in a long time.