Probably nothing confusing. I think yours is like mine, it has been opened at the factory for some reason, or maybe it has waited for being packed for a long time. There is really no way to know for sure. Mine definitely looks like it may have been repacked at the factory due to cosmetic failures (then again my first X also had cosmetic failures even it was obviously not repacked/waited for packing a long time, so it may be just the way QC is today). They of course have a way to reseal them in a way that it will acts as new, just as it should be when you buy it from store as brand new sealed. There is not magic in that. They probably and likely can even update and use these during tests at the factory without going to activation process what normal users are required to do.
How's is your battery working? Mine is definitely stale even it is not as old as yours, so definitely this procedure may have negative effect that buyer has to suffer from. From now on, if I ever buy iPhones again (pretty disappointed with the quality these days, it is far from what it used to be in my previous iPhones), I will demand to see the serial number first and check the mf date myself, or buy from places with liberal return policy. For a 1k I expect nothing but top quality, if it was like 1/3 of that what similar competition phones cost, I would lower my expectations.