Vertical integration is just such a gross shop model, at least for me...nothing is more unappealing as a consumer than walking into a bike shop and being bombarded by Bontrager/Specialized bars, stems, saddles, shoes, clothes, helmets, tires, pumps, etc. A local Trek dealer has slowly gone this route in the past three years, and it has now reached a point where I won't even really bother going in to buy stuff. They used to have a nice selection of shoes from Sidi, Shimano, Pearl Izumi, & Lake, but now it's wall-to-wall Bontrager junk. Clothing has gone the same route. Castelli, Pearl Izumi, Hincapie, et al replaced by the terribly dull Bontrager stuff.
Maybe my memory is playing tricks on me, but it never seemed like inventory stagnated when they were selling from a variety of companies. Merchandies seemed to move. But now, this Bontrager crap sits there forever. It seems like their inventory never changes, and this seems to play out when I'm riding my bike. I NEVER see people using this stuff save for the people who bought complete bikes. I know for a fact the shop owner claims he can't buy inventory like he did a few years ago because of the internet, but honestly this model seems like it a temporary fix to a larger problem.
The whole gray market BS must be super frustrating for shop owners, but getting back to the OP, I don't think a viable solution is to take these frustrations out on paying customers whether that manifests as being a ****** with customers wanting to install gray market parts OR crippling your inventory for the sake of comfier margins.