I really don't think there is one, sorry. Not every abstraction can fit snugly into an easily-swallowed piece of setting lore.
Honestly, I'm moving away from racial HD more and more. Sometimes you want to scrap the "12HD = base attack +9, Fort +8, Ref +4, Will +4" formula, or whatever. Sometimes you want a CR5 encounter with a Huge or Gargantuan creature, or something with 200hp but a base attack of +6.
You're born with racial HD (although most creatures get more as they age), whereas you have to "learn" class HD.
You're born with racial HD (although most creatures get more as they age), whereas you have to "learn" class HD.
Pretty much this... racial HD are a representation of your innate toughness and resilience by merit of your race, your instinctual skill, and natural talent... class HD on the otherhand are the result of dedicated training and study.
Then how do you explain 0 racial HD races? They can’t have no HD when they are born, as then they couldn’t be considered living creatures, but when they are born, they definitely have no training at all, so no class HD.You're born with racial HD (although most creatures get more as they age), whereas you have to "learn" class HD.Pretty much this... racial HD are a representation of your innate toughness and resilience by merit of your race, your instinctual skill, and natural talent... class HD on the otherhand are the result of dedicated training and study.
These are your BASIC basic races, and you kinda gotta think of these people from 0HD races as you would non-trained-whatsoever 0-level conscripts for war (commoners with no measurable combat training, like farmers and tradesmen from w/e race). They might technically have 1-3 hp, but as soon as they get hit with even 1+ damage, they're out of the fight whether they're over 0 HP and conscious or not; they simply don't have the stomach to continue fighting like someone who has had combat training/experience.
This is kinda where you as the PC comes from: the progeny of a mother/father from this base pool of commoners from whatever 0HD race you choose. And the combat-training you receive in your backstory sort of establishes your first level of training in any proper Class, and thus establishes you the PC with your first 1HD, such as being a level 1 fighter.
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Edit: TLDR - The difference between Racial HD vs. Class HD is the difference between "A Commoner" of that Race vs. "A Hero" of that Race.
I don't.
The only byproducts of HD are hit points, saves, and skills... all of those things require zero in-game explanation. Spells that care about HD don't care if those HD are racial or derived from classes... it's just an arbitrary number.
So what if two humans/whatever have different skills or different strengths/weaknesses? It's almost like real life. Why does one person die falling in the shower, and another survives skydiving with a faulty parachute? Who cares? Lol.
What advantage is there trying to explain why twin human A has 155hp whilst their twin human B only has 100hp? When would you EVER have to explain why two twins have different saves?
Twins with different HP are a perfect example. Consider that a lvl 12 Fighter with 12HD and 155HP has a commoner twin with 0HD and 2HP, and either of them gets Coups De Graced with a 1d4 dagger, a dagger through the Eye or Throat is still instant death to either of them. HP from HD is an abstract representation of being able to shrug off or avoid damage from experience and training and to keep pushing through the injuries before becoming unconscious.
Except a coup de grace with a basic dagger will only do 1d4*2 + str.. and the 12hd fighter will make a fort save of ~18 and just take ~8 damage and the commoner will die from the damage and if not most likely fail the save...
Yep, and that person survived being shot 17 times, whilst this one died from a bee sting. It literally happens. There is no need to explain this phenomenon in a fantasy game.
Templates are wierd, especially when applying them to playable characters, rather than monsters.
In your particular Half-Dragon example... if you don't have racial HD, your 1/day breath weapon does 0D6 damages... trying to explain or rationalize that in game, or out of game, is freaking impossible. Whoever wrote that template either needed to make it only for monsters, as in having racial HD is a prerequisite to accepting the template, or it should be based on total HD regardless of origin.
Except a coup de grace with a basic dagger will only do 1d4*2 + str.. and the 12hd fighter will make a fort save of ~18 and just take ~8 damage and the commoner will die from the damage and if not most likely fail the save...
It's 10+(1d4+str+everything else)*2 = Fort DC, but that's not the point, the point is that it's instant death regardless of how much HP he has left. If he miraculously makes the save, then you keep slitting his throat or twist the dagger in his eye next round or until he doesn't save.