It does not seem like it, but that is often the way it is with collectibles. If they have original packaging they can often be worth not just more, but much much more. I predict that guns in provable "original" boxes or packaging are eventually going to be worth disproportionately more, i.e., a like-new gun without box is worth $500 and the same gun with the original packaging worth $1000. Just wait, watch and see..... It makes little sense, but that's the way true avid collectors (of many things) think.
I'm glad that the store and the consignor made the adjustment for you. It was certainly appropriate under the circumstances.
I am a little confused by the destruction of the box. Once the box had been removed from your transaction, it was no different than any other box in the store or any other item belonging to that consignor. The box certainly had value, just not as the original shipping container of THAT gun. Apparently, the store owner had the consent of the consignor to destroy it...and you can draw your own conclusions as to whether or not that indicated some complicity on either of their parts.
The original problem discovered in this transaction was not that the gun was sold in the box; it was that it was sold as "new in a box that was its original box".
The packing containers for older, valuable items obviously have a value of their own, even when empty. That is true whether we are talking about the box for a Registered Magnum or an antique child's toy. That is due to that fact that 1) they were made of less sturdy materials and therefore often didn't survive into the present and 2) since their primary purpose was to protect the item until it reached the end user and consequently, the end user generally threw it away. So when the collectible is rarely found in its original container, it is highly valued.
When a box that is correct for the piece (not to be confused with the original box) is found, most collectors like to add it to their collectible item. That DOES NOT mean that it is as valuable as the original box nor should it EVER be passed off as such.
To continue to use the Reg. Mag. example, it is common to attribute the value of an empty blue box as $1000. When a Reg. Mag. is placed in that box it easily raises the value of the package that much or more; even though the number on the bottom does not match that of the gun. If that same box was discovered to have the SAME number as the gun, the value of the package is raised significantly over the individual value of the two items.
In the case of the sale under discussion, even if it had been advertised as in an original box, that would also have been incorrect, just as if a Reg. Mag. had been sold in a blue Outdoorsman box and sold as in "an original box". The value of the destroyed box probably had a value somewhere a little south of $100. But if someone actually had a gun that would have been "correct" in that box they might have paid more for it.
Bob