Security are unlikely to care. I've taken some boxed phones through on various occasions and there was no problem. I suggest you separate it from your other items to reduce the chance of it making a bag "too complicated" causing secondary search. You won't be the first person that hour to be carrying a new phone in their bag.

From the point of view of a clear scanner image that can be evaluated quickly and found free of threats, a phone in a box with neatly wrapped accessory cables visibly separate from the device is far better than a tangle of cables next to and around a device - which is how most people store the electronics in their bags.