Godot 4 will feature support for multiple windows, as in actual real windows. Earlier versions didn't. The popup in godot 3 is just a "GL surface"/control node rendered inside the window as a overlay over other control nodes and the rest of the view buffer. So yes, they are very different.
Games normally wouldn't use multiple windows like that, this is more to benefit the editor which itself is built upon godot engine, but this will also benefit others who use godot to develop applications rather than games. You might be surprised but there are other purpose/genre specific game engines with editors built with godot but also image editors, in the past I've even seen someone work on a 3D content creation suite with godot as the basis.
