As someone in retail, online inventory is often off, which is why calling in is a good idea especially if the store's a long ways away. Asking for visual confirmation is a good way to ensure that the product is there. Customers want to believe that we have the product they want, though, and whether it's over the phone or in store I get many people every day going through the denial stage of grief when they hear that their precious product is not in store.
I don't think it's the call itself that's annoying, that's just a smart thing to do, it's the customer being an ass towards the employee that's the issue. Like when a customer asks to double check the back, they can ask politely & reasonably or they can be a complete ass about it and act like we're squirreling away half the store out of sight.
In this case it's the customer acting like the online inventory is the be-all-and-end-all arbitrator of what the store has in stock and then belittling the employee (who has 0 control over the website, stock, or pretty much anything) for being "wrong"
When I managed to escape the anglosphere for a while I remember going to restaurants where I would order something and they'd be like "Naa, we don't have it." It was really quite refreshing and it was a joy for me to just get what was convenient to cook as opposed to having some complicated logistical system to get me a treat. I want to patronize more taverns where they give me a bowl of what's hot for a silver coin.