I would venture to guess the low level api is useful if you want to get Havok or some other non-built in physics engine working. Not every game fits into the same 2d pixel phsyics mold. You can't ship such a one size fits all solution with a general purpose game engine like Godot.
There's no requirement to use physics in Grid, just as there's no requirement to use physics in LÖVE, which is what the engine is built on.
We build the game engine from this approach because most games want "maps," and "entities."
We use a Quake-style architecture because even if you're rebuilding a 2D version of Tabletop Simulator, you're going to want a map and entities.
We'd rather have a one-size fits all solution (worked for Quake and Source pretty well) versus a Unity/Unreal style flashy game engine where you're suckered into still doing all the work yourself, but hey PBR looks good.
