In a number of cases -- handyhands being the case that triggered the issue for me -- the automatic crafting selection algorithm produces circular results where it just continuously boxes and unboxes items.

Adding

      allow_as_intermediate = false,

to the nullius-box-* recipe prototype (boxing.lua:65) disables the automatic hand boxing of items as intermediates. As far as I know, there are no hand recipes that use boxes, so this should have no side effects.

Items can still be boxed by hand by directly triggering the recipe; it just won't do so automatically.

I'll experiment with it. I think there are higher tech recipes that use boxes though. And this would mean that it would give you much worse results when trying to show you the total raw materials, since anything in a box would just stop there and not show you anything meaningful.

Is there an interface for blacklisting recipes for HandyHands specifically? If so, that might be an approach.
There is a bug posted from a month ago on HandyHands about someone running into a similar situation using that mod with Nullius, except in their case it wasn't boxes, it was reversible mirror/priority type recipes.
As far as I can tell, the vanilla game handcrafting behavior is smart enough not to create these loops when you handcraft. So that makes me think this is a deficiency with HandyHands specifically that it will consider loops like this. I'd be willing to help HandyHands out by marking the recipes if the interface is easy enough, but it should also be possible to detect these situations on their end, detecting when a chain of recipes will consume as much or more of the end product than it produces.