I'd generally agree with you, except for the fact that we'd have no recourse if we were shorted a hit in a box. For example, let's say that box 3 has an extra hit, so we sit it aside to be randomed between the base slot holders after the break is over. Then we find out box 8 only has two hits - then what do we do?
I think we should just go in order, and if there's extra hits after all 15 boxes are opened, we will random them between the base slot holders.
I don't think it will matter; I opened about a half-case worth of these last year and didn't have any issues with extra/shorted hits.