DD9 is encountering this less at the 5th grade level, but in previous years she was getting things that made little sense. We were pretty sure they were teaching innumeracy. DD openly rebelled, and so, too, did her parents.
My first question to the teacher would be, what on earth are box methods, and what possible utility could they have? A quick google turns up a box method of multiplication that looks like the inverse of a "partial quotient" division method that caused much consternation in our home. I'm a STEM worker, and I could not independently parse that nonsense. Once I did some googling, I figured it out enough to realize they were demonstrating how to turn a 5-step division process into a 20-step process, and creating more opportunities for mistakes along the way. So we revolted, taught DD long division the standard way, and she never looked back, except with contempt.
If your DS can reliably perform long multiplication without resorting to box methods, then that's what he should be doing. The point of all this is to show the children that there is more than one way to skin the cat, and they should use the one that fits best for them. Where Common Core math implementations go horribly wrong is in insisting the children be able to use all of the methods correctly, on demand.