I am not sure why this is happening, but after a few minutes of running a project all of the editor functionalities move to a new window separate from the original process window. For now I can just keep it minimized, but it is pretty irritating to have this clutter all the time.
Even weirder is that I get a strange graphical glitch when trying to play the game in-editor. In this image, you can see that for some reason the usable area of the editor shrinks down to a windowed mode when in full screen (the area outside of the topmost window is just a non-interactable frame).