I've done it both ways but prefer not to do the cuts.That's probably more proper than what I do. I usually just set a rafter on the top plate and use hurricane ties without cutting those out.
I can't disagree with any of that.I would suggest 6x6 as opposed to 4x4 for longevity, strength, and resistance to bumps/accidents. Birds mouths are easy to cut and figure out as well as providing a more stable rafter, making easier to nail and spreading the load, are you in a snow zone?