What you are conflating is the mechanism by which each system operates. One uses optical pulses, the other uses radio signals.
The Nikon CLS system (more properly called the Advanced Wireless Lighting (AWL) when referring to the wireless aspects of the CLS system which also encompasses all of the Nikon flash system including the hard wired uses of flash) uses optical pulses to communicate with the off camera flashes. The source of the optical pulses is either an on-camera flash or on camera near-infrared controller. In either case the on camera unit must be a "Commander" in the CLS/AWL system.
The Godox X1 system uses radio signals to communicate. So do most other third party wireless flash systems.
Canon has moved from an optical system to a radio system for wireless flash control which they call the "RT" system. Some of their flash equipment can operate via either radio or optical protocols so they can be (at least partially) compatible with the older optical wireless flash control.
Nikon recently introduced a radio controlled flash that is only compatible in radio mode with a couple of the latest camera models. It is also compatible with Nikon's optical wireless system.
Even when everything is radio operated, different systems won't usually work with each other.
Sometimes third party systems will reverse engineer a primary manufacturer's protocol. The Yongnuo RT system mimics the Canon RT system and most Canon and Yongnuo RT devices are cross-compatible. After a new release by Canon a firmware revision is sometimes needed by Yongnuo to maintain that compatibility.
Sometimes a third party maker will have more than one system that is either not compatible, or only partially compatible, with their other systems. Yongnuo's rf602/rf603/rf605/YN560 system is for control of manual flashes. Yongnuo's YN622 system is for control of TTL flashes. Older pieces of each system won't work with each other. But since late 2014 the YN622 pieces can be controlled in manual mode by the YN560 system.
Godox is relatively new to the wireless flash scene. Like others, they've also had a couple of different wireless radio systems in the past. Like all of the other third party suppliers, they've experienced their share of growing pains.
With their X1 series they are building a system that allows manual flashes, TTL flashes, and studio flashes to all be controlled via the same wireless radio system. Obviously the manual flashes don't magically become TTL flashes when controlled with the X1 system, but the X1 system does allow the same controller mounted on the camera to control the different types of strobes.
With an X1 controller you can control all of the Godox flashes with X1 receivers built in, such as the TT600, TT685, V850II, V860II, AD360II, or AD/XR600 series. With an XTR16 or XTR16s receiver you can also use an X1 to control older Godox flashes such as the V850, V860, AD180, AD360, AR400, RS600, and various Godox AC powered studio lights.
What you can't do with the Godox X1 system is control flashes from the Yongnuo, Canon, or Nikon radio systems without using an X1 receiver attached to the flashes in question. You may or may not get full usability in such an arrangement.