Configuring Root Domain on FlightControl with CloudFlare
Instead of ALIAS -> Root Domain, setup CNAME -> Root Domain on Cloudflare. CNAME flattening · Cloudflare DNS docs FlightControl
Apparently FlightControl team didn't know this was possible

I reported this, and then they replied:

Well, I guess this is the charm of working with an early stage engineering product team! You also contribute to the product as a early adopter.