There is some truth to the notion that new bikes are a break-even for most shops. Storing the bike and assembling it, and then paying overhead, wages, taxes, utility bills, and insurance, all eat up that margin.

Most of the revenue at a bike shop comes from parts/accessories and repair, where the margins are much higher. Your LBS is counting on those two revenue streams when someone purchases a new bike in person, because they're not getting much if anything from the bike sale itself.

When Specialized takes inventory from the dealer chain and slots it for D2C sales only, they are effectively saying to the dealers, we don't need you. We prefer to sell our product ourselves, but we realize that not everyone will want to buy direct from us, so for the meantime, we're stuck with you. But we're certainly not going to make life easy for you, so we're squeezing you on margins.

I predict that this strategy will backfire, and that Specialized will have two problems - disgruntled dealers who don't want to sign up for squeezed margins, and potential public backlash if the experience without the dealer in the chain doesn't go exactly right.