I've worked in a gaming store similar to GameStop for a year and a half and I've seen a couple of trades between customers right on the counter. Personally, it didn't bother me at all and I never asked them to go outside. Most of the time, I talked with them both and gave them information/value of the games they were trading as they asked for my advices and if it was a fair trade haha. I mean, I was not the manager, simply a part-time as I was still going to school back then, so I didn't care much. I'm not losing money, clients are happy, they will come back and buy again anyway and to be honest, I didn't really care if the store didn't get the games as they were generally not rare/interesting games.
My boss never complained about it either. It's not as if it happens all the time, or a dude just keeps filtering people coming in to get all the games before the store.
The only thing our boss ever said was that we should not personally offer money to a client before he knows how much the store offers and declines that said offer. Then, if we wanted to offer, we could, but we had to do the trade outside our working hours. I haven't personally offered to a client but one of my coworkers did twice if I remember right and he just met up with the client over the weekend to get the games. The boss knew about it but it was okay with him.
Honestly, I really encourage this, as it makes both parties pretty happy. This way, the person coming in to sell their games gets more money and the buyer gets a good deal. Win win situation and I get to chitchat with happy customers. Win win win situation.
Also, I've had people coming in to trade Zelda, Mario Party, Mario Kart, Pokémon, etc. games on the GameCube pretty often and we were giving $0.10 (no, that's not a typo, yes, it is 10 cents) store credit (back when the store focused only on new games and was trying to get rid of GameCube, Xbox and PlayStation 2 games. Now they don't do this anymore haha). Most of them agreed on that cheap offer as they didn't know the value of their games. I always told them something along those lines : "Are you seriously going to trade in those games for $0.10 each? You may not know this, but your games are worth a fair bit of money, you should probably take a look online or at another store that is more specialized in retro/old games as we, unfortunately, focus on recent games.", and generally, they were pretty happy about it and thanked me for my honesty.
So yeah, in the end, I guess it all depends on how you perceive it and how the store clerk does.