There are already sources for boxes other than USPS, which can be shipped First Class or Priority (or Express, Registered, and International, for that matter).
$3-5 each is incredibly expensive for a shipping box - especially if you are talking about Small Flat Rate size. How do you figure there is reduced chance of them getting lost due to some clever packing trick? Same question for damaged. Your statement seems to suggest that losses and damages are largely due to thieving postal workers.
How is it an alternative to padded zipper pouches? Are you suggesting that the shipping box would be so awesome that people won't bother with the pouches? Perhaps my initial reaction to the idea has to do with perspective. Are you thinking about folders, fixed blades, or both? Yes, padded pouches can be less than ideal for storage - part of that is because people/companies don't use the appropriate size. (It gets expensive buying multiple sizes, I get that, but shipping a folder in a pouch that could hold 4 or more similarly sized knives usually means that the pouch will be set aside on receipt.)
Can you share any of those sources? I threw away all my pouches when I started using a Pelican case because I originally planned on never selling any of my knives. But things change and I recently sold a knife on Ebay and the buyer complained about me using bubble wrap. He gave me a negative 1 star rating and said something like "No case, no pouch, no nothing?..on a thousand dollar knife? Seriously? If this is how you treat your customers...I'm going to warn everyone on the forums..blah blah" He got even more mad when I requested him to reconsider his rating because I never said the knife would come with an aftermarket knife pouch and his negative feedback was solely based on something I never mentioned in the description.
Almost every nice knife does arrive in a knife pouch regardless of who you buy it from, so it's reasonable for him to have the expectation of getting a $4 knife pouch with the purchase. However, how he handled it was unreasonable. I thought about putting "This knife doesn't come with a pouch" in the description, but I've never seen another post that says that in the listing. But it's probably because most do come with pouches.
Yes, I know $3-5 is crazy, especially when there is no benefit to the seller, but to keep it short, without profit, the product can't exist.
The reduced chance of loss with clever packaging- If I had the answer to this, I would have put that in the post. I'm not withholding trade secrets or high value business ideas. However, as far as solving business problems go, I don't think this would be an insurmountable challenge. Unless there was a demand for the solution or you were going in to this type of business, coming up with the clever packaging is probably a waste of time.
As for how or why knives can get lost during transit, your guess is as good as mine. I always use computer printed labels because I have bad hand writing, so if there is no possibility of being delivered to the wrong address due to bad hand writing, what else could it be? Even if it was delivered to the wrong address, I think the majority of people would return it to the post office, give it to the mailman the next day, track the sender down using google, etc. I don't think the majority of people would even open a package if it's not in their own name. So if you think about this, it's unlikely it was delivered to some random person and then that person not return it. Plus if it was delivered to the wrong address, I think the tracking system they have enables them to narrow it down to the local carrier who had the package on their truck since they have the "Out for delivery" status. I've tracked down packages all the way to the carrier before and I was shocked but they actually even remembered exactly what I was referring to, probably because they work the same route every day and even know all the people. I have 2 different mail carriers that come to my house and I'm basically friends with them, so if something got delivered to me, they would remember if it was within a day or whatever, if I can describe what it looked like etc.
Damaged? The options are cost prohibitive. But I'm just talking about any type of cost effective padding inside or a zip lock bag and padding. There is no other cost effective or realistic way to prevent damage during shipping.
Alternative to pouches- These would be square in shape, so they would be stackable which is easier and more efficient for storing than pouches that can't be stacked without side support.
Sizes- That's why $3-5 is a range. USPS and other companies have size requirements so you make the smartest decisions you can given the estimated usage. But this practice would be a waste of time without a demand, even if it's easy to figure out.
So what boxes are you talking about that you use? Do you buy them or is it from some other item you buy frequently? I need to buy a few because I've run out of all the boxes from my everyday purchases. I use bubble wrap most of the time, but I have some more expensive knives that buyers might not be happy about if receiving the knife in bubble wrap.