Most of the time if it is refurbished the put a sticker on the box and also under the battery of most phones. Other than that they don't hard code it or anything like that in to the OS.
What version of Android was loaded when it first booted, before updates? Sometimes, if the phone is up to date, it might be a sign... New in box often comes with the original version it had when the phone launched.
Yeah, different OEMs do things their own way, of course, but the fact that you had to update it is a good sign. I am guessing that for refurb units, once Motorola (or whomever handles them) is done with it, they would load the most up to date factory image, rather than the launch image. But don't hold me to that.