That 3D anime head doesn't connect to the neck the way a real head does (the back of the head is more complex than just a ball), and with a chibi style like in your drawing, the situation gets even worse since chibi heads can't connect in a believable way.I wouldn't worry about it. If you were to connect the head realistically, it'd be too far forward. If you connect it so the head's in a realistic location, the neck will appear too far forward. If you lower the head to hide the neck's location, the pose will read differently from what you probably intend. I think your first edit is fine. You could perhaps move it forward by another pixel without it looking too weird, but it's not going to look good to everybody no matter what you do, just by virtue of chibis making no anatomical sense.
