I've seen middle grounds where the box itself was made with waxed cardboard (with wrapping). Not sure if this is necessarily better. Only few items I've seen are sold in unwaxed cardboard (and I suppose it depends on the food contained).
I don't know how to calculate which alternative is the least polluting, but it's not obvious at all that lack of wrapping implies less pollution in the big picture.
As I wrote, this is not obvious. Leftovers require energy and resources to produce, transport, and possibly destroy. Energy and resources imply pollution.
This is very similar to the plastic vs. glass problem. One intuitively thinks that glass is better, but when transport pollution is included in the equation, glass is not necessarily better anymore.
Fruit and veg just doesn't need wrapping - but you do want a way to keep stuff you're going to eat raw from touching gross stuff.
Plus I’ve seen small stores in London restocking loose fruit by breaking down small multipacks quite often, at least here in the center around lancaster gate/bayswater.