AV,
You nailed it, the rule for patchbox alignment is they are all different. If you are building a copy of a particular maker, or school you could base it on proportions from an original. If you aren't making a copy, then place it where it pleases your eye. Tape it in place, hang it on the wall, look at it tomorrow, etc., until it looks good to you.
The placement in the pictures looks pretty good to me.
-Ron