There was indeed a period where the box store mowers from JD and many other brands were not the same as what you would get from a dealer, despite sharing the same model number. The box stores created this problem, by their buyers naming the price they would pay, and leaving the manufacturers having to find a way to try to meet it, or lose all sales through that chain. Walmart does the same to their vendors, common practice.
I know from speaking with the dealer about this, that JD ended this practice at least several years ago, mostly due to dealer push-back, as the dealers were the poor bastards faced with making warranty repairs to these inferior products.
But having said that, I always thought the differences between the dealer versions and big box versions were more about smaller things, like replacing ball bearings with sleeve bearings and bronze sleeve bearings with plastic sleeve bearings, etc. I never heard that they had fundamentally different body or frame components, but have to admit I never asked that.