I don't understand your subject line in this context though, could you elaborate there?
In-store is a different scenario. There's cameras for one thing. You will often find you still have to sign that you got money back, there's often a manager that has to come over and approve the refund or you may be dealing directly with people in the return department, who often have a fair bit of seniority, may have had a stronger background check than regular employees, those kinds of things.
I'm just saying, low level employees, esp. when they're bots, very often do not have unsupervised customer refund ability for overcharges, and it's at least partly a loss prevention thing. Empowering them to provide a discount on a 2nd sale and allow the customer to do a free return on the old item is calculated by the bean counters to be a lower risk proposition.
Also, I actually have been to stores where they say "you have to return the item, then we'll resell it to you with the appropriate discount" for something like this. And it's for this same reason. In some cases, their systems simply just don't allow outright 'refunds' without the product coming back into the company's possession. I'd guess their theft insurance costs probably go up unless they have restrictive refund policies, too.
People in general underestimate how much of a problem employee theft is for corporations. Of course, they steal back, I'm not crying that much on their behalf, and it still sucks for the customer, I didn't mean otherwise