There are several engineering officer's on the Defiant and DS9. Who else do they report to? O'Brien is in charge of both.
Are you sure they're officers? Muniz was a crewman in the
Defiant's engineering crew. There were other crewmen about, too. And we don't know that the Bajoran engineers were officers, do we? We know Rom was an enlisted engineer in the station's engineering crew.
If they wanted to go the NCO route they should have portrayed him more as an NCO. They could have shown him frustrated by taking orders from a young new officer or even guiding a new officer. His character on DS9 could be wearing LCDR pips and you would never know the difference. He's just another member of the senior staff. The closest he's ever been to be being portrayed as an NCO was as a transporter chief on the Enterprise.
O'Brien, frustrated? Why would he be frustrated by an officer - the station gave him enough grief as it was! He'd hardly notice an officer giving orders to him. Besides, Starfleet is "supposed" to be more egalitarian than the US military.
I can only imagine that O'Brien was assigned to DS9 because he was one of the most experienced people when it came to Cardassian technology, probably due to his experience with them during the border wars. And, as before, it wasn't really settled that O'Brien was enlisted until about the 6th season of TNG, when Lt. j.g. Barclay orders him around. They
did work it out later, and he
did have crewmen under his authority later on in the show.
It's not a perfect explanation, and it's going to seem odd when compared to modern military practices, but hey, we don't worry about whether officers have noble blood nowadays, either. In the future, they'll have different priorities.