I agree with you 100%--but this does put the breweries at a disadvantage if the distributors and retailers don't care squat about the proper handling of beer. Most of these individuals approach it from the perspective of the megaswill--which is pasturized and/or treated with products to increase shelf life, as well as having the advantage of moving off the shelf fast. Most retailers don't understand the fragility of most microbrewed beer, and couldn't care a less about it either. I wish they all knew and cared, but they don't. I'm not sure if having a contest like you advocate would change their minds, as long as most of their business is the megabrews.
Like anyone who is going to have their work scrutinized more carefully on a certain day than on an any other average day, they are taking extra special care to do the job as perfect as possible for the event. This doesn't mean that the recipe is different (i.e. special ingredients, etc.), but extra care is taken to make sure the batch has as little mistakes or flaws as possible. Compare it to an average day on any job, versus that same day with the boss looking over your shoulder all day. I bet the day with the boss looking over your shoulder is different than the other days (not much, but different).
Being a homebrew judge, I would venture that the difference between the "special batches" and the "standard batches" would be little to none, with the little differences being minor flaws that would escape the palate of the average consumer. Not that the average consumer has poor taste buds, but these judges have trained their palate to pick up very subtle off flavors and aromas, and that is what they are looking for in these beers (most all of these beers in a given category are "good", but the judges need to rank them best to worst--basically nit-picking subtle differences between each beer). The average consumer would enjoy either version, and probably not notice the difference (if any).
If anyone ever managed to get a contest like that off the ground, I would be excited to see the results, and put the results to good use in buying my beers.
Kevin