Better to factor it into the pricing - whether it be on the shipping end, or the price you put on the animal. If I'm buying something from Average Joe Reptiles, and they inform me that there is going to be a box or handling fee, I am more inclined to say Thanks, but no thanks. I sort of look at it the same way as I view somebody saying I have to add the 3% for a PayPal purchase...the difference being that I can't turn the box charge person in for violating a TOS, lol.
I don't use the pre-made kits...there are several reasons, but one of them is that they are expensive. Once somebody is doing enough shipping, the convenience factor weighs in more heavily, and it makes more sense.
I, personally, don't like reusing boxes; first impressions mean a lot, and layers of tape, or ripped paper (from removing the old tape) just don't do it for me. I'm not so anal that I complain about receiving that type of box; but, in my mind, it says something (its hard to define just what that something is - I've given it a few minutes, and failed). I guess, to an extent, it sort of depends on the situation. I HAD to reuse a box when I shipped my adult dumerils - it was a large box from Mice Direct, with the styro cooler inside. The dimensions were such that I couldn't easily come up with an exact replacement, and I was set on using the cooler (3 adult boas, with a combined weight of nearly 60 lbs, requires a sturdy box)... I'd selected that box because it arrived in perfect condition, and I'd used extreme care in opening it. I didn't like doing it, though.