On which reality should the character base his decisions?
If an NPC has me at knifepoint, should I be terrified of the instant lethality of cutscene knives, or should I scoff at the woeful inadequacy of gameplay knives?
This, I agree, is the sort of dissonance that should be kept to a minimum.
Generally, I opt for the reality of the cutscene, because gameplay mechanics are often looser interpretations of reality. I don't believe that I can actually carry around 100 health potions in my sack or that my mage can still stand after taking the brunt of a hurlock alpha's axe or that a bard's song (a non-magical attack) can somehow stun enemies or that the battle I just participated in consisted of my character kiting a carta gang leader around the room for 3 minutes. That doesn't really make sense to me, so I imagine that the real battle looks a lot more like a cutscene. My rouges aren't just getting a single sneak attack and spamming wierd abilities, they're dancing around the room, throwing tankards and upturning tables, my tanks aren't getting stabbed hundreds of times, they're glancing attacks off their shield and pummeling enemies before they get the chance, and my mages aren't starting wild fire tornadoes inside wooden buildings, they're weaving controlled spells that only hit the bad guys (or just guys if friendly fire is activated).
Sure, I could try to pretend that a reality which followed the gameplay rules of any game existed, but I don't think I could deal with the inconsistencies that would eventually arise. Even ignoring the cutscene problem, I just don't see how certain story premises could exist in a world where people can apparently take multiple axe swings to their body, have those wounds combust, and still walk away fine.
So should you be worried about being held at knifepoint? Of course, because that can only perceptibly happen during a cutscene, and cutscene logic states that knives are dangerous. However, if you wanted to have the scenario occur during gameplay, you could pretend that a rouge that gets you down to low health has subdued you at knifepoint if it pleases you.
This doesn't explain inconsistencies like the kinetic barrier problem, but that's just general negligence on BioWare's part. Ideally, that stuff would improve.