That's odd, I just edited a wp-config file using the file manager today and it worked perfect. I've been on proxied Cloudflare forever, maybe I excluded the file manager from being affected by CF firewall rules to fix it. Or maybe it was fixed on V12 if you have Apache on control panel server? Someone who it is not working for should try firewall exclusion.
I just made a WAF custom exclude for uri that contains "filerd" or "/websites/". And I have a page rule for "/filerd/" that also has security disabled. Note that the firewall excluson has alllll the check boxes ticked for exclusions.