setGeometry() is a convenience. It’s a tiny bit faster than your Python code, since it’s implemented in C++, but this probably won’t make a practical difference; and the convenience of having it do exactly what you want may outweigh the convenience of having it already written for you. 
Note that in either case, your mouse pointer will be bound to the render frame rate, which is fine if your frame rate is high, but kind of crummy if it is low. It may be better to set the hardware mouse cursor instead. Panda provides a limited interface to do this, via the WindowProperties structure, though it’s not a great interface.
David