Well, this is the same problem that we have with almost every role playing game ever created. If a bullet hits you in real life, it doesn't matter how experienced you are, you won't be fighting very hard for very much longer. But being able to suspend our disbelief or assume that, in a fantasy world, wounds aren't handled in the same way, adds to the total diversity of combat and unit possibilities. I've played pen and paper role playing games long enough to accept this paradigm.
But this isn't a role-playing game, even if it has role-playing aspects. Combat in role-playing games revolve around a very small number of participants, and so being able to do things like survive being shot in the chest is necessary for combat not to suck.
But combat in Elemental is going to involve tons of units. Each of those little units should die if an arrow hits them in the face, or if someone catches them with a well-aimed sword stroke. There is no reason for regular units to be able to survive ridiculous things based on experience because we have large numbers of them. In an RPG, if my character dies he dies - that's it. In a game with dozens, hundreds, and thousands of units in play at once, it's not the end of the world if they, as individuals, cannot survive a lightning strike for example - because there will be more left.
If you need a creative resolution revolving around bolts of lightening being fired, you might assume that a warrior with more HP knows when to "duck and cover" or how to carry himself into combat to begin with in order to minimize damage from magical effects (prepare my armor so that parts of it that might conduct electricity aren't touch my skin, etc.)
That's just silly. Can you imagine reading a book where an experienced battalion of troops goes into combat walking like freaks and overall doing really bizarre things to minimize contact with their metal armor in case of a lightning strike, something else in case of a fireball, etc? I'm sorry but that'd would lend any fun. And what about someone wearing leather armor? What's an experienced leather armor wearing soldier going to do to make him more resilient to lightning than the green recruit? Hide under a rock all throughout the battle?
It is obviously not the end of the world if experience provides extra HP to regular troops, but it's not intuitive at all. For heroes, sovereigns, fantastical creatures it is more believable. But I know that no matter how experienced I might become in medieval combat, none of it will help me survive a lightning strike better than the next guy. And I imagine the regular people of your kingdom to be just like you or me; they don't have magic, they aren't magical in any way...
