I'd be interested in some of these that come from legitimate shops (for instance, doesn't Toys R Us and Target both maintain Ebay accounts? I know less reputable sellers like GoHastings do as well) I wouldn't be nearly as quick to trust these if some lone guy was claiming to sell these at reduced prices..... not unless you are into bootlegs or gravel wrapped in newspaper.
I've ordered through eBay many times myself. I did Season 5 of Sons of Anarchy, Season 4 of Downton Abbey (hey, I appreciate classical drama), Season 4 of Justified, and Season 1 of Da Vinci's Demons...all were legitimate copies, Region 1, with official artwork and the disks were genuine. How the resellers get these...I do not know. All I know is the resellers that handle these sales have long-standing reputations that are marked quite high. To answer your question, some companies do have eBay accounts (Best Buy and Newegg, for sure).
What you also have to understand is that the price companies buy these shows at is always much lower than the price they sell it at. These resellers on eBay sell their copies at an initial price, and as the orders come in, they adjust the price lower to offer a better deal, but they keep their markup and shipping costs as reasonable as possible so they can still make a profit (places like Amazon and Best Buy sometimes offer a release date deal that still makes them a sizable profit, though). In the case of DVDs, with how cheap many new releases on film hit as of late ($10-15 vs $15-30 on Blu), its a trend that shows that while Blu-Ray is becoming the eventual standard for entertainment on the market, DVDs are still strong enough in popularity to sell.
Basically, go for the resellers that offer returns and have real solid reputations on eBay. When the product comes, compare it to what is online (aesthetically) and check the barcode number on the back with the official release. A bootleg is easy to spot (generic DVDs with shoddy artwork and possible 'burn' hints on the bottom; the artwork on the outside of the case is cheap and the packaging is cheap and flimsy). Boardwalk Empire, for example, has some of the most solid packaging for any TV box set I've ever seen that isn't a special edition (this is true of all of HBO's recent releases); Justified and Sons have been solid too for standard sized packaging; Once Upon a Time, sadly...I went through Amazon for Season 1 and Season 2 when Season 2 released, and I've had two shipments come with the plastic damaged; it felt cheap in my hands and they used plastic tabs (the * style where the lil arrow tabs push in toward the center), and I am sure it'll be the same with Season 3.
I am sure there are others on CAG that have done what I did and can vouch for the legitimacy of it.