Tractor supply doesnt make a big box looking for 24 X 24 X 48
Just because they don't have them in the store doesn't mean they can't get them. They can call the companies that make the boxes for them and can get what you want if they make it.
It won't have the Tractor Supply logo, because those are branded and only popular ones they normally stock are branded. The two manufacturers they used (or used to use) was DeeZee and Delta, it would have one of their logos on it.
Also, special orders would have to be shipped specifically for you, and it is usually $200+ to UPS/FedEx to the store. They should be able to cross-dock through one of the TSC distribution centers (manufacturer puts it on next shipment to DC and the DC puts it in the store lane for the next truck). Cross-docking usually took 2-4 weeks to make it through the system, but it was free to do it that way (other than the cost of the box).
All this is from experience working there. I was with them for almost two years, but I left April of this year and can't guarantee that nothing has changed since then.
On a side note, we have a store called Northern Tool that is more of an industrial supply store and they have this style box as well, and I believe they manufacture their own toolboxes.