cool article, in games there is always a toss up between plausibility issues and liberties taken for the sake of game-play and design.
The amount of power swung around in turn based battles makes it very had to believe the same gang need to go around looking for keys to get rickety wooden doors, or lack the ability to resurrect characters that die during story events.
Unlimited Saga had a system a bit more like the "realistic" hit points like you describe.
a character might have 200 or so hit points but about 7 life points.
It's been a long time since I played it but essentially the general hit points were lowered when receiving attacks and when using special skills, and they replenished when a character was resting (or not being used for a few turn or walking about in between battles)
Then "life points" (if I remember correctly) represented true Hit-points; the lower your general HP, the more likely an enemy attack would also claim a precious Life point or two, representing that your character is too tired to avoid, parry or better absorb an enemy attack and that the attack was either serious or fatal.
I always though JRPG's should have a system for "knockout" and also "death" as opposed to either knockout only or death only.
If in one RPG Universe when you reach zero HP you're dead and pheonix downs fixes that, then how come when a character dies in the storyline someone doesn't just chuck a phoenix down at them?
then if in another RPG universe if zero HP means Knockout, well what about when a Death spell successfully hits? That character hasn't been clobbered into a coma to later be given a drink of water, no, the grim reaper visited the screen and took his soul to hell; it should be game over.
If I were designing a turn based RPG I would have stamina point and life points, to designate Knockouts from "death" (i.e. game over)
Stamina points meaning your general physical well being; lose some if you're exerting yourself or get hit by a general attack, when you lose them all you get "knocked out" i.e., clobbered unconscious.
Where as on the other side, Life-points (or "life point" if mortal) would be 'game over' material if a character dies then they're dead.
Some might say this is too abrupt, but there's lots of ways around this. If you imagine a game that has interactive timed events (like the Limitbreaks from FFX, or Squall's gunblade from VIII) it would be cool to imagine an enemy suddenly using a Death spell, and not just knocking out an ally but killing them and because someone on your team has a quick reaction skill, before the death is permanent you're given a brief opportunity to act quickly to save the game over.
This way, the "lore" of the world (in this imagined RPG) would be consistent even should characters die as part of the story, but also it would allow resurrection magic to exist only for it to be a matter of time like CPR on a drowning kid.
This way the RPG world using this system could have a death spell, a resurrection spell, general knock outs from physical assault, and narrative based death of character without clashes in plausibility.