It isn't that the story and gameplay work off of separate tracks - it's that the gameplay can't actually affect the story at all, even as far as being able to move your character to where the next part of the story should happen.
And I believe that a game is better when the gameplay and story affect and reinforce one another. The idea is very relevant to this conversation.
It's ludicrous to claim that this necessarily happens in D&D. When it happens we call it "railroading", but it doesn't happen all the time, and neither is the system set up so that it must happen.
The idea that gameplay and story can affect one another is much bigger than railroading, though that is one place where a division between the two crops up. "It doesn't matter what you roll, you fail, because the story says you need to fail."
Plus, no one's claiming it that it necessarily happens in D&D.
Rechan said that gameplay and story, in his view, should be kept on two different sides (he used a moat and a brick wall, but a wrought iron fence made of tigers has a bit more zing and means the same thing). I vehemently dispute this proposition -- I think that a game is better where the two mix, rather than when the two are kept separate. It is in taking this proposition to heart that 4e has strayed away from being a game I want to play or DM (specifically, that affects my DM side more).
One way that 4e has taken this proposition to heart that is relevant to the profession/craft system is that it provides no gameplay for it, keeping it entirely in the realm of "story" (which, in this case, is DM Fiat). The story might care if you're a blacksmith's son, but the rules don't.
This is the other side of that division. Railroading can be when gameplay doesn't affect stories. This is an example of when stories don't affect gameplay. They are kept separate by the wrought iron fence made of tigers. This is deeply unsatisfying, largely for the same reason: when I'm playing a role-playing game, I expect my game to affect my role-playing, and my role-playing to affect my game. Not to be divided.
It is a better experience, for me, when they are unified.
When the wrought iron fence made of tigers is taken down.
So I prefer a game where story and gameplay aren't on either side of a wrought iron fence made of tigers. 4e has a few examples of this being true, and it is deeply unsatisfying for me. None of those examples are really "railroading" in the sense that you talk about, but the concept behind railroading and the concept behind DM Fiat being enough for Profession/Crafting skills are similar on a pretty fundamental level.
Obviously, I'm not the only one who has the opinion that this isn't a good thing, at least in this case.