I have no direct knowledge on this one way or the other when it comes to Deere models, but non-warranty/supplies might be the difference if there is one. The tractors get crated in and have to have final assembly. Things like batteries, belts, oil, blades that would not be covered by warranty could be stipulated to be supplied by the BBS at a lower margin than "genuine Deere" parts - especially since they have these commodities in stock at the Box Store.
The models sold at the Box store are definitely built to a price point to compete with no-name models, building on the Deere name. But that price point would be of interest to any dealer in the market, whether Box store or Deere dealer. I would think that custom mods to Box store models would drive up the price - exactly the opposite of what you are trying to do.
The "price point" Deeres (no matter where you buy them) are built with compromises to meet a demographic model - nothing wrong with that and doesn't make them a "bad" machine. Just don't expect them to do something they were not made to do or to last as long as more expensive models. A Ford Fiesta and a Porsche 911 are both cars, but you expect different levels of performance, price, quality, durability from them. Same thing....
This is nothing new... Quite a few people walked away from Deere when they began to go after the light duty residential market many, many years ago instead of making machines just as "durable" as their agricultural stuff - long before the box stores. "These new models will only last for 10 -15 years or so, not like the REAL JOHN DEERE machines!!!"