I'm a 10 year vet of retail computer sales.
Your wife's experience is not uncommon. Saying the difference is the look of a system is not wrong - there's plenty of computers that I sell that are rather weak, but are decorated with lights and aggressive plastic to look more gamer-y. And then you got a rather basic looking computer that actually performed rather well.
The sales person issue is common - you don't know who's wearing a blue shirt. It could be a stocker, a manager who doesn't actually work with tech, or it could be a many year season vet like myself. It is a random roll. Don't ever be afraid to ask "I am trying to buy a gaming PC, do you have anyone who's especially versed on the topic?" - Most store workers will not mind passing that off. A store like Best Buy is not commissioned, meaning they're trying to reach revenue goals. They'll get it to the person who can get the most Revenue per hour, which if you ask that, will likely be the person who knows the most. Also, Best Buy specific: If two people help you out, if you do buy something, ask them to please include the first sales person on the sale if they treated you respectfully.
The go-to-a-different store problem you had is not uncommon. My store right now, for instance, does not carry gaming PCs - we are rather small and in an area where GPCs just don't sell much. The big store 30 minutes away does. When we do a local pickup order, it has to go to the other store, get recognized, then get picked and put at a register. It definitely happens where we have one left of a computer, order it, then it's in the process of being sold. It's an annoyance, but it's how things work. It is not an organizational or logistical problem usually, it's just bad luck. In your case, at least they called.
Also, lay off workers for offering the extended warranty. It's part of the sales, in a lot of stores it's how sales people make money individually (the computer might go to the store, but upsells like that might be part of personal earnings). It is not hurting you listening to it. If you want to make a sales person just hate you, cut them off when they're selling something like that. Someone does that to me, you're guaranteeing you I'm gonna press on everything then because my biggest upsell is gone, so I gotta try for everything else - Office, Internet Security software, power options (power strips and UPSes), cables, cases for laptops, ect. Let me finish and say no thank you, I usually assume you've got a budget. But I still have 2-3 things I have to hit (usually Office, Internet Security and Warranty). Let me do my job and we'll get done faster, and you just might get something you could need but not know.