Both Lt. Commander and full Commander are called "Commander" just as Lieutenant j.g. and full Lieutenant are called "Lieutenant." Troi was a Lt. Commander when the series started. When not addressed as Counselor, she would have been addressed by her rank. Both Lt. Commander Troi and Commander Troi are appropriate.
She is promoted from Lt. Commander to full Commander in that episode. After that, she sports three full pips, instead of two gold pips and one black pip with gold outline.
There is a screen cap in HD from Generations with Deanna right before she crashes the bloody ship. She is wearing three full pips ... as in, full Commander.
At that time, Data had not taken the test to become a full Commander. So, Deanna outranked him.