Agree, my gut thought is if you bought directly from Ikonpass.com, and go to ski.com they're still going to be willing to take your money and treat you the same as you bought it from them. Especially if you deal on the phone, and drive a hard bargain on pricing; they'll click that mouse around for you if it seems they'll lose the sale.
As far as exclusive Ikonpass only itineraries, the heart of those deals, typically are available from each partner resort anyway who give you the bundlepackage or seasonpass rate on lodging, but without having to buy the bundle; If you bought outside of ski.com, I don't think they're going to turn you away from the best promotions they have available if it means losing $$$$ of sales.
That being said, if you know exactly what you want, and think you might use ski.com's services, why not buy from ski.com at exactly the same price; to get the option for those benefits even if valueless?
On the flipside, if you think perhaps you'll need to adjust your passes over the summer (e.g. buying base pass but then fee upgrade to full pass) it maybe safer to buy direct from the source and cut out middlemen who might mess it up.