I just got off the phone with my local GameStop, and the very nice employee there explained to me exactly what happened yesterday with Breath of the Wild preorders. I'm not sure what your GS experience was yesterday, so some may already know this, but I haven't seen any threads.
If you went in to preorder BotW: Master Edition, you may have been told that "the SKUs are messed up", and so your receipt showed the regular Switch version, but you were actually signed up for the Master edition. That's… not entirely true. Officially speaking, no one has the Master edition on order.
I'll say that again. Not a single person in GS' systems have the Master edition on preorder. That's because Nintendo never gave them a SKU for the Master edition. As far as their systems are concerned, it doesn't exist. They don't have stock numbers, either, so GS doesn't know how many are available for their customers, nor did the stores have a way to cut off preorders.
Reps may have told you this, but anyone who wanted a Master edition preorder got a note on their Power-Up Rewards account attached to the preorder. Corporate is able to search all accounts for this note (it's most likely some sort of #tag in the body of the notes field of the account, so it can be easily searched for). Whenever GS gets stock numbers and a SKU for the Master edition, they'll be searching all accounts for that note to assign units. The problem is, GameStop still doesn't know how they're going to do it. It could be in order of the timestamp on the receipt (in which case, West Coast is screwed). It could be first come first served; by that, I mean that the individual store have been given provisional instructions that they may need to manually call customers with that tag on their account to confirm their orders.
Until that happens, not a single GS customer has a confirmed order for the Master edition. If they end up having to call customers, and you miss their call, there's a good chance your order is screwed, if that's the route GS decides to go to clear this up.
So… that's where we stand now. 🙁