when an officer is attached to a storm trooper unit, what defense die does he/she use?

I can not find any ruling on this.

He uses the defense dice of the unit he is in. You don't have to confuse the commander version with the personnel upgrade version, they are 2 different things

From "Upgrade Cards" on page 55 of the RRG:

"Trooper upgrades add specific trooper minis to a unit, represented by unique sculpts to easily identify them. These minis always share the defense value, wound threshold, and weapons of the unit card they are equipped to, but may have an additional weapon of their own."