Using Y as up is pretty popular for 3D engines, it's not just Godot. I mean, it is sort of arbitrary, and some engines do it different, but the popular convention for stuff like OpenGL, DirectX, Vulkan, etc. is to have Y up (but as I said, it can be anything, and even with Y up there are left and right-handed coordinate spaces which confuse things further). I think Blender does something different and it is infinitely confusing to me, every time, since I am accustomed to Y up.