If these experiences are correct, then something is happening beyond simply producing the CO2. It's possible that the evidence is simply flawed, though. It's hard to collect proper data about brewing, especially in homebrewing processes, and there are plenty of examples of even experts drawing incorrect conclusions. But I'm rather inclined to trust that the anecdotes at least indicate *something* is changing.
My non-scientific hypothesis on why bottle conditioned beers tend to require a stabilizing period is not related to where the CO2 molecules are, but rather where the nucleation points are.
Let's start with shaking up a soda bottle or beer bottle for that matter. When you open a carbonated beverage that has been shaken recently, it gushes. Why? It's certainly not related to an increase of co2 molecules or pressure. It's caused by the presence of bubbles that act as nucleation points that wouldn't be there in a restful state.
When you bottle condition, you have yeast and other foreign material floating around in the beer from the moment you bottle. These particulates settle out in the bottle, after the carbonation process is done and further (and faster) when you finally chill the beer. If you open the bottle after the CO2 was created but before the particulates settle out, you end up losing a lot of the Co2 due to the nucleation points. Now, let's not ignore that the chilling step is equally important due to colder liquids holding on to more CO2 when the system is opened. However, I'm specifically talking about why a bottle conditioned beer that has been in the fridge for a week or more obviously has a more stable carbonation than one that is simply made cold in 24 hours.
If the hypothesis of "the beer needs more time to absorb the co2 in the head space" held any water, it wouldn't cause gushing. Gushing is only caused from massive amounts of Co2 coming out of solution in a short time frame. In other words, it's contradictory.
I'd love to be able to experiment more on this stuff if I had the time.