Costco does this for a lot of things. They keep the expensive stuff locked in a secure room. When you bring one of these to checkout, someone gives you the thing you purchased.
I don't know anything about retail logistics but I imagine this model helps prevent theft, and it's more efficient for their layout to have them all in a little corner so they don't take up much space, especially when some of these are console bundles.
They'll have games, gift cards, restaurant coupons, movie theater tickets, spa coupons, etc. A lot of the times too they'll sell these gift cards cheaper than what they actually are (i.e, they'll have a $100 Steam card for $80). So for them it's less "these are just digital codes why bother" and more "let's do this semi expensive electronic/experience thing the same way we do all the others".