> I have no problem with it myself; but the companies/brands certainly do.
actually, the companies don't have a problem with it, the customers do. customers (it's human nature, maslow's hierarchy, etc) cling to their beliefs about themselves and their identification with products that reflect their values. Companies would rather cut costs and sell one-size-fits-all products, but they need to give customers what they want, and different customers want different things.
> Lots of national brands have a "this is not produced in a factory or machine that produces any store brand"
and many people have the need to think that they are "better" than store brands, or more likely on HN, that they "see through" all the marketing, so companies market to you "transparently"... if a brand says "this is not produced X way" and you didn't even mention X, hmmm, do you really think they haven't figured you out?
if you are the cheese puff king, the most expensive thing you can do is not sell everybody exactly what they want, and you probably have redundancy in your manufacturing facilities, so why not segregate which products are on which machines, so long as a market segments aren't too small.
Lots of national brands have a "this is not produced in a factory or machine that produces any store brand".