I don't have a definitive answer with citation, but I do have a bit of a military background in a NATO country that's kinda flag-obsessed, so here goes: The NATO flag is used on NATO installations - SHAPE, NATO Headquarters, that sort of thing. And when NATO events take place elsewhere. Never seen it flown with just one other flag.
I've personally only seen it used in Denmark at BALTAP HQ in Karup, a godforsaken rain-drenched airbase in the middle of nowhere. In Danish flag protocol, the NATO flag is considered "overnational" and when flown with several nations' flags, it is given precedence. (As would be, say, the International World Scout flag at an international scouting event.) BALTAP was a joint German/Danish thing on Danish soild, so the order of precedence was NATO, Denmark (host country), Germany.
The NATO HQ in Brussels is an example:
http://www.nato.int/cps/en/natohq/topics_49284.htm
SHAPE (military HQ for NATO) has this entertaining write-up - the NATO flag isn't the problem, but keeping everybody else happy
is. The member flags are rotated daily, to keep the peace - and even that led to infighting.
https://www.shape.nato.int/page12967543
Flag protocol is ever a tricky business. Note how instead of flying the NATO flag higher or bigger, it is simply placed centrally.