Maybe there's some technical reason for it being the way it is now, but I see no reason why bread loaves can't be kept in boxes with the bags inside of the box, like crackers. The bag would still be re-sealable, the box could be only loosely 'sealed' to allow air circulation, and the bread could be visible through a plastic window much like pasta boxes. Instructions inside would indicate to customers that the box is optional once opened.
Some might argue that it'd be wasteful additional packaging, but having worked in a grocery store, I can attest to the tremendous waste from bread getting squished in bags and having to be thrown out. Boxes would have far fewer occurrences and allow nice, organized stacking.
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I wonder what it would cost? Presumably, that's the only difficulty. If the box were made with a laminate of plastic, perhaps you could for-go the internal bag. I can see this being good.
How about a reusable corrugated plastic sleeve? You take it shopping with you, and put your bread into it, or return it to the store for re-use.
Really, they aren't needed. Bread is packed on stackable flat crates.