what is not being considered is the preparation often starts with a volume of reactant on the bottom of a vessel slowly dissolving according to physical soluability.

if you start a reaction like that without stirring, you will see a big difference in product yeild.

Anyone who has done any level of chemistry, including home chemistry, has observed how important stirring is to dissolution. If you just dump some ingredient into a container with solvent without stirring, you're going to end up with undissolved solids on the bottom covered by a heavy super-saturated solution. Over a long enough time with changes in temperature, or heating from below causing convection, you'll eventually end up with a uniform solution. But if you need the product for some purpose, waiting an arbitrary time maybe isn't the best plan.

I think you're talking past each other. From the article: "Because you pretty much always stir your reactions, even when all the components are in solution right from the start - right?" Dc is saying that people stir stuff because its not properly in solution yet, and then they just don't turn it off because there's no particular reason to. Maybe somebody who understands chemistry better than me can figure out how relevant the experimental procedures from the supplementary material are to this scenario, I can't really make good sense of them.