Barring the feats you mentioned, the scenario you put here is a rather specific instance, and not really common occurrence, don't you think? What about enemies with <Medium impact weapon damage, like melee and crossbows? What about characters who can't get the most out of heavy armor because being a hybrid of dodge-evasion and medium armor like riot armor/tactical vest/infused leather armors?
Most of the damage you'll take will go to your energy shield and disappear. Most of the rest will go into your armor, unless you're just terrible at the game, because you'll set yourself up so that you only allow the attacks that your armor will mitigate. For example, if you're a tac vest wearer, then you'll allow the pistol/SMG characters to live to the very end of the fight because they'll be doing 0s. Riot gear? Let the knife-wielders do their thing, it's no big deal. Leather armor? You'd better not be letting yourself get hit often or you're playing poorly and need to work on that, because leather armor is for mobile, far-field, or stealthy melee type characters.
No, I don't think it's unusual. It's a case where enough damage hits you that it breaks through the two main lines of defense. It shows how feeble that final line really is, but you can mix and match numbers to your choosing, if you feel I cherry-picked too much.
Barely out of Depot A, did the Maura quest, got those very basic shields and metal armors, then followed the rails to Rail Crossing and while exploring, opened that door and let the sniper take his shot? How's that go? 300 damage again, but your shield only blocks 40, and your armor, basic as it is, is only giving you 30% DR? Then 300 -> 260 -> 182. Conditioning stops 36 then! But you still took almost 150. Either that was the only hit you took, in which case your Advanced Health Hypo fixed you up, or you took several hits and died anyway. Either way, Conditioning still didn't make a difference, because it's such a small effect.
Your question about metathermics is exactly what I described in the second-to-last paragraph of the previous post. It's where Conditioning looks as good as it can, but it still doesn't make a meaningful difference. Though, of course, there's no reason to take metathermics damage before getting an energy shield, and even a basic energy shield will result in enemy metathermics doing very little damage to you, much like a shield damps the bite from frag grenades and mines.
If I were going to change Conditioning, I'd make it a Per + Agi + Con feat, and reduce its percentage reduced, but have it apply
before shields and armor. The idea would be, you know how to avoid the damage that comes in; you're not necessarily more inherently bulletproof, you're more adept at rolling with the hit, ducking slightly at the last moment, turning your armored shoulder into the bullet. Such a feat, even if its percentage were small indeed, would act as a magnifier of both your shield and your armor, meaning it would be a defensive power multiplier. It would let your shield last (slightly) longer, and would give your DT a tiny bit more opportunity to keep you safe. It would, in that order, then be useful, if not necessarily terribly powerful. But, your idea of tying it to Tempered obviously makes a lot of sense, too.