It is safe to assume that none of the abilities that are unlockable by players through spending skillpoints are ever found on rare BOs.
There is one exception that I am aware of and that is Attack Pattern Omega III. Aside from this one, I never saw an unlockable ability on a rare BO.
Engineering player exclusive skills are, well, those unlocked with skills in the engineering area of the player skills.
There are a couple that I recall from the top of my head: Emergency Power to Shields/Engines/Auxiliary/Weapons III, Directed Energy modulation III, Extend Shields III. Possibly Reverse Shield Polarity III as well but not sure about thatone.
There are probably more but those are the ones I recall seeing in the player skill tree that can only be gained by engineering players.
So, would it also be safe to assume that if any BO has a III ability, we cannot train those ourselves?
so im a Tactical off on an Escort as ive stated before and ive maxed out the requirement for HY3 but i cant find it anywhere.
Hit "U", select the BO that you want to train the HY III ability (actually selecting any BO will do), click on the "train" button at the bottom of the window. HY III should be listed there. Clicking on it brings up the train-interface known from the BO power store/normal BO trainup.
Edit: if this does not work for you you will have to file a bug report. The above is the only way I know of to train BOs unlocked skills.