There was an announcement, and the closest documentation is Public Network Services · Fly Docs (archive) but I agree that it is unclear. (I suggested some related doc changes but they haven’t been made.)
fly deploy used to display an error message if fly.toml contained non-standard ports and the app had a shared IPv4 address (announcement, example); maybe the error message was removed/changed, no idea if it’s intentional – might need fixing. (A random guess, since I can’t check right now: The fly.toml on which I got the error message had a single [[services]] section with public ports 80 (http), 443 (tls+http), and 5000 (http). Your fly.toml has two [[services]] sections, maybe the error checking code doesn’t detect that case. If so, it might need to be fixed.)