I agree it's not all that common but they are definitely out there. As for whether you could build those with Godot's engine I have no idea.
Moving outside of your editor absolutely blows, and the less you do it, the better it is. Unless the alternatives are thousands of times better (nothing comes close to Substance Painter, and tools like Houdini still do some things better than internal tools for example. And of course, well, 3D modeling is still a hellscape of zbrush and Maya.), you just stay in with your tools. Nothing sucks more than having yet another editor and needing to have a pipeline to keep everything in sync.
It's not about needing crazy physics calculations directly in your engine (although your particle system being affected by it can do cool things), it's about not having to deal with yet another tool that fixes one problem and brings in 20 more.
Also, as said, the days of fully scripted movement are pretty much gone. There's physics interactions any time you have vehicles involved unless you want to feel it slide around and feel like crap, for example.
Most commercial games have scripted character movement (every FPS, RPG, strategy games, basically almost every genre) and the only physics objects are random falling objects that don't affect gameplay... Cloth simulation, cool but can be faked and doesn't affect gameplay. Ragdolls, only really used when characters die and again, can be faked.
So name a single AAA game that actually uses proper physics for anything gameplay related?