I suppose they could've put fine-print wording on the packaging similar to what was done with Season One. Something along the lines of, "Certain shots could not be located or were too badly damaged, so alternate takes were used."
Also, perhaps these takes were chosen for other reasons.
I notice, for instance, that in the original wide shot on DVD you can see a boom mike in the upper left (it's more noticeable in motion). CBS Digital would just have erased it or re-framed the shot downward as they have done on so many other shots in S1, but perhaps HTV was too lazy to do either, so they just picked an alternate take!