The project aims to provide high-speed internet to areas that don't currently have access to it using self-navigating balloons. While this concept may seem a bit absurd, Alphabet has had success with Project Loon. The FCC filing in question was to assist in relief efforts in Puerto Rico -- the regulatory organization granted an "experimental license" last week, allowing Project Loon to provide emergency LTE service to the devastated island. The company is currently working on integrating with Puerto Rico's local networks.
Alphabet has a history of spinning out successful companies from under its umbrella, such as Waymo, Nest and Access. If they are indeed setting up Loon as its own company, it shows great faith in the product, despite the fact it's only been used and tested in a limited number of places.
Update: Alphabet declined to comment on the FCC filing, but gave us the following statement which pretty definitively states that Project Loon is still part of X: "Project Loon hasn't spun out as a separate organization. Project Loon is still a project at X."