Geek Squad agent here. I wouldn't be worried at all about purchasing an open box item, especially a GeekSquad Certified one. The difference between regular open box items and Geek Squad certified ones is that on the certified ones they literally have to be perfect! Any dent, scratch, flaw, even overly worn or missing packaging and it can't be certified. Generally the certified ones are only ones that people returned unopened or at least in brand new condition. The certification process is stupidly long and takes about an hour for an agent to go through and tests all hardware and cosmetics. It is securely wiped and reloaded. (we have a copy of all OS X DMGs on site). Most employees purchase the open box ones because because they are lower than what best buy gets the product for therefore lower than our employee discount.
ONE THING TO NOTE! It is really hard to move these high dollar open box items especially if their geek squad certified because often its just not a big enough discount off of retail! Ask to speak with a manager and haggle them down a bit! They usually will move $50 or more on that big of an item just to get it out the door!
And worst case scenario, for some reason you buy it and decide it would be worth it to you to get a brand new one, you have 15 days to return it.