This basically means they are using userspace Wireguard, such as the go implementation. That is as opposed to the in-kernel wireguard.

The reason to mention conjuring a TCP IP stack out of thin air, is that most of the time the operating system is providing the tcpip stack as part of the kernel. With wireguard go, the tcpip stack is running in user space, meaning it can be created in a normal user space process such as the flyctl command line interface. This is indeed quite magical for people who have been around for many years as a usable in-process userspace tcpip stack is a relatively new and a novel thing.