You shouldn't be able to stack multiple copies of BO abilities, even on separate officers. There's a few good reasons for this:
1) Many abilities that are totally fine and balanced when you have 1 copy become insane with multiple copies. Feedback pulse and reverse shield polarity come to mind. RSP has a huge cooldown, which makes it feel pretty balanced when you have one copy. You can get out of tight spots, but it's not always gonna be there for you. Multiple copies make you invincible to beam weapons. And if you're fighting a PUG, it's god mode.
2) It makes no sense from the standpoint of the ship doing something. All the officers are controlling the same ship. If the ship can only overload a torpedo once every 60s, I cannot fathom how telling the officer next to you to push the same button on the console would expedite that process.
3) Some abilities are just flat-out worse than other abilities. Aux to structural integrity field is worse than engineering team in pretty much every way. Right now, this is dumb. I can stack engineering team, so getting aux to structural is useless. If I can't stack abilities, those abilities that are flat-out worse just become a diminishing return system for stacking similar abilities.
4) There's no need for it. It homogenizes gameplay, and there's never a situation where you NEED to stack an ability.