If you get jumped from behind then the eyes or throat aren't going to be available targets (unless the person jumping you is clueless), and neither is the groin (depending on how they grab you, and again if they know what they're doing). I like your thought process of going after vulnerable/vital targets, but position is going to determine which targets are practical.
In the case of being grabbed from behind, none of those targets are likely going to be accessible (again, assuming that the attacker knows what they're doing). And in the case of being struck from behind, your number 1 priority should be to protect your ability to continue fighting (ability to see, breath, and think) long enough to regain your bearings and launch a counter attack.
Assuming that the instructors are actually skilled though, and are used to training with things like eye attacks, groin attacks, etc... then they would likely be aware of those targets and position themselves to protect them. Sure, they might get a little dinged up, but the student is likely going to realize that it is them and it was just a drill before anyone winds up in the hospital.
I like the drill personally, and (assuming that the students are ready for it, which I think you could argue that Parker is) it is more telling of what the student will actually do in a high stress ambush attack type attack than if they know it's going to happen.
Aside from that, what if the student "knows" that it's going to happen and then actually gets attacked? There is the risk that they'll think that it's just a drill and not fight back 100%. Not a great mindset to instill in someone IMO.
I'm not sure who first said it, but I've heard fighting compared to jumping into a pool of ice cold water. At first you go into shock, your muscles tense up, you are disoriented, confused, unable to think or act like you normally would. But then your body starts to calm down, to deal with the reality of the situation, you start to regain your ability to think and to act more deliberately.
It's that initial "shock/ambush" phase where most good street fighters/attackers/criminals will try to finish you. They know that the longer the fight goes, the more the odds tip towards the more skilled fighter, and they don't want to take the chance that this might be you.
It's also that phase which should be addressed first IMO from a self defense standpoint. If you can't survive that phase and get to the phase where you can actually fight back, then it doesn't matter how good you are at the "active combat" stuff.