You’ve said that later volumes in official APs tend to use more high-threat encounters than earlier ones. I wonder if this is in response to the party’s expected composition and itemization. You’ve also suggested that not having the runes makes combat feel like it does at lower levels. What that says to me is maybe a party with striking runes should be treated as a higher level for encounter building.
I've been under the impression that's, in practice, already baked into encounter design, but it can be nothing more than an impression. My personal feeling is that the earlier official APs were simply distorted by the writers subconsciously keeping the lessons from D&D3e/PF1e and thus choosing more high-threat encounters reflexively. (This is separate from the problem you mention of groups that don't engage with the tactical mechanics as strongly as is assumed; it seems to me that any encounter generation method is going to have to assume things one way or another when the mechanics actually reward doing so).
I'm saying that I have only found Extreme encounters in later books, not in earlier. (Meaning books 4-6 of a given AP)
My own theory is that this because the game slowly tilts the balance in favor of the characters. I'm basing this on two things:
1) the book specifically says Difficulty Classes become easier as you level up. I'm thinking this hints towards a general trend.
2) experience. The heroes feel noticeably more competent and powerful vs level-appropriate foes at high level. At level 15, the Fighter and Cleric got the Scare to Death ability, meaning they can reliably one-shot any foe not shielded by Incapacitation. Level -2 creatures truly are mooks now, whereas at low level, they felt more like the characters equals.
Case in point: the Barbarian just now defeated an opponent of her own level (16) in single combat, something that would be nearly unthinkable at low level. Granted, this Barbarian is probably the game's most extreme damage-dealer there is - I'm not confident any other character could have pulled that off. And the player wasn't exactly unlucky with the dice. And it was a very close call - she sports, what, 230 hp with rage hp, and ended the duel at well below 50 hp. Yadda yadda - doesn't change the fact she pulled it off - she did defeat a named level 16 NPC all by herself, me as the GM holding nothing back: that NPC even "cheated" by biting her before the duel started, inflicting an Enfeebled condition that lasted throughout the fight.
So no, I can't say I think the party's composition plays a role here. I mean, I don't think Paizo expects that to change as heroes level up. (Are you thinking of my half-joking suggestion any Wizard player first roll up a warrior and only at double-digit level switches over to the wizard?)
Itemization: well, I feel confident the game is balanced on the assumption the treasure guidelines are followed, so... Yes, the heroes have access to striking runes and whatnot. I'm basically giving them what the adventure says to give them.
What I'm saying is that I imagine that if this exact party were deprived of their fundamental runes, then monsters would revert to their earlier role. This is because if heroes start to find it easier to hit and damage foes because the overall balance auto-shifts in their favor, removing the potency and striking runes will make the game balance fall back into its earlier state. I don't see any indication that parties with striking runes are meant to be considered non-standard.
"earlier official APs were simply distorted by the writers" I honestly feel they were just following directions = the encounter-building guidelines of the Core Rulebook (page 488-489).
That is, I don't blame the adventure writers. If anyone is to blame, it's the CRB writers. Those guidelines are
very harsh on level 1 heroes. I can easily see value in adding a bit more sophistication to those rules - essentially saying they work best for levels 7-14 (very roughly).
At levels 1-6 you might want to treat encounters as one category more difficult (so that in place of a Severe encounter, you merely place a Moderate one).
The biggest beneficiary of this would easily be level 1 adventurers playing by newcomers to the game, exactly the kind of player you don't want to scare away by repeatedly killing off her character! But even veteran gamers at level~5 would, I think, be only grateful... And at levels 15-20 you can treat encounters as one category less difficult (so in place of a Severe encounter, you can go ahead and pitch an Extreme one).
Not saying this advice is scientifically perfect. But it would mean that newcomers would have a better time, since they invariably start at low level. And it would also mean that the tendency I'm spotting in the official APs gets written into the guidelines (=they already do pitch Extreme ones where a Severe one would have been used in earlier installments). Note: I'm not saying you should double dip - which you will if you upgrade the written AP encounters. I'm talking about enshrining the encounter guidelines the AP writers seemingly already follow.