Danishes are mechanically modeled (what I meant to type, by the way, apologies) in only the very loosest sense of the word. The Profession skill only generates money. The Craft skill can generate items, but if you're creating anything that doesn't already exist by D&D rules, it has no real mechanical attributes besides type, complexity and price. In other words, such an item might be useful for roleplaying or storytelling purposes, but mechanically, it's only good for resale.
Perfectly true, if you want to make a pastry that mechanically has a type, complexity, and price. Our hypothetical baker doesn't, he just wants the flavor, which has no mechanical properties.
Storytelling concerns are entirely flavor elements, as they have nothing to do with what D&D's system mechanically models. The SRD would be pretty hilarious if it included Craft (Cooking) DCs by which every monster could be "defeated," though.
More to the point, I honestly wouldn't have any problem as a DM letting our hypothetical flavor-based baker's fluffy creations satisfy those kinds of challenges. The best way to articulate my reasoning is by example: per RAW, any character whose background fluff includes spending their entire life in one town (over 100 years for an elf) will know only the most ludicrously basic things about their hometown unless they invest in Knowledge (Local), which will grant them a comparable level of knowledge for every town on the face of the planet. When the issues at hand are about the story and its progression, rather than making gold or dealing damage or something else that actually affects D&D's mechanical system, I don't see any good reason not to indulge players' flavor. In fact, if you restrict players' flavor from having any influence on the events of the story, you're discouraging them from coming up with any flavor in the first place. Taken to its logical extreme, forcing mechanics to dictate the story turns every single conversation in the game into a diplomacy, bluff or intimidate check, without any actual roleplaying involved. Not exactly thrilling, and not exactly playing as intended.