So far, no one yet has actually addressed the topic's question about store exclusive edition items.
From what I've noticed, games which are multi-platform receiving these kinds of edition releases such as with Limited Run Games and NIS America, the physical game is packaged separately from everything else advertised. So, to me, what is actually being advertised isn't authentic, as the received order is instead a standard game that also happens to be mailed with some added bonuses in another container. This is far different than edition items of years past. Were I someone who purchased these items, I'd also take issue with many of these items, namely from the two aforementioned publishers, advertise these items as some "limited" edition, but the packaging doesn't state this detail anywhere. In rare circumstances, an outer label of sorts may be affixed outside of sealed copies only or perhaps be found on the mailing packaging itself, but it's much more rare for the actual item to be detailed as such.
Like you've mentioned, distribution seems to be handled poorly. In this day and age, I don't think there is any clear way to prevent scalping. But, something similar to how Sony first handled PlayStation 5 distribution through an online lottery of sorts to later send random participants a link to a queue where they're then only given the chance to order their desired item seems far more ideal than simply setting a product order page live for bots and scalpers to take part. Or, if there is instead a preorder window, then at least the total number of orders would be manufactured at a minimum for those reserving it, with however much excess available for standard ordering.
These sorts of items will seldom be in stores now. The profit margin is much higher through online preorders, as opposed to manufacturing a preset number with an undetermined amount of overstock later being heavily discounted. It is this same reason why even some standard games don't receive typical retail releases and will surprisingly (at first it was, anyway) instead be online exclusives to third-party publishers such as Limited Run Games.
