Sure one can develop a game without an engine like Godot or the other big ones. It may even be easier to do so, for a given case, and more flexible and performant anyway.
I am not talking about platformers or shooters or doing what everybody else can do, if it comes to simulation most engines I know are out of the question, or need such heavy internal programming that again an own framework may be quicker and easier.
Actually, the few games I like do not rely on an engine (Factorio, Orbiter, the X series, ...), or use in-house engines or frameworks. KSP was the only one among those that used Unity, and I have the feeling that curbs its development by a lot.
If only I was a real(tm) developer :-)