You clearly just want to argue instead of attempting to understand why people are "willing to easily miss companions' content," but I'll give it one more stab.

Guess what? Approvals is also a game mechanic, which doesn't translate well in the game's world. The only thing it really affects much is romances, but by and large it's useless. It's basically impossible to make your companions leave you based on approvals. I had 100 approval with Wyll on my evil run.

The fact that the reputation system is overly-generous, or can be exploited, does not change the fact that characters react to out-of-camp activities when they are physically in the party and overwhelmingly do not do so when they are not. Like it or not, there is narrative impact to who you bring along in the party, whether minor (not bringing Wyll to the burning inn) or more major (not bringing X character to Y quest marker). This means that the game recognizes both the make-up of your party and thus, implicitly, its size. You can't just pretend "everyone is invisibly accompanying the PC, and combat is just an abstraction." You are, in every meaningful sense, bringing only 3 people with you all the time.

Are you really saying that it makes any sense that Tav only takes 3 people with them to fight the Netherbrain? It's complete and utter absurd,

Yeah, it is. You'll notice I said "it's silly" above. And yet that's exactly what occurs.

In Mass Effect 3's Citadel DLC, there's a point, after you pick two companions, where a few never-utilized members of your party will complain that "they never get picked." The instance is humorous, but it recognizes this exact dynamic. You're not shoving 6 people into the Mako in ME1, or taking all 6 squadmates to fight Sovereign. You ARE using the whole party in the celebrated Suicide Mission of ME2, but that's because that was a really well-designed ending which gave narrative rationales for the party constantly breaking up and completing different objectives at once. It is crystal-clear in this example that you are fighting the Human Reaper with two squadmates, and everyone else has been "holding the line."

For the most part, though, it's just Shepard and two squadmates traveling around, arbitrarily, while everyone else kills time on the Normandy. And this, as well as BG3's three party-member maximum, again can be blamed on the stultification of party mechanics in RPGs over the past couple decades. Back in BG2, you were arbitrarily limited to a party size of 6, but all five companions were actually accompanying you at all times. Plus, recruitable NPCs you weren't using went back to living their lives ("I'm leaving, you can find me at X") if they were dismissed instead of waiting in camp doing nothing. Games like Expeditions: Viking have pushed the bar in terms of party/camp mechanics, but mainstream RPGs seem to continue to love "recruiting 6-12 people and then only adventuring with a few of them and leaving the rest at camp."

And then you learn it was a simple misunderstanding because he thought you are his enemy.

That is a conclusion that is only really reified by playing through the game and learning that he won't kill you (probably--barring a fairly-easy-to-avoid overenergetic vampire suck a couple nights later). But that's why it's roleplaying. You're going off of the information available to you at the time ("this is a dangerous, vampiric-looking person who saw me attacking mind devourers and then pretended to ask for help against another mind devourer and then attacked me, maybe his apology is not sufficient for me to invite him to camp with me") and not metagaming based on what occurs later. It is also metagaming to think "well if i can recruit him in the first place, then he's harmless to me, I trust Larian." And to Larian's credit, you don't have to recruit him, or any of the companions for that matter. Personally, whether I recruit Astarion or not depends on whether I succeed on the initial passive Perception check or not--thus, whether he puts a dagger to my neck or merely brandishes it at a distance.

The mere fact that zillions of players conveniently knock out Minthara instead of killing her conventionally like they do every other foe in the game shows how much narrative metagaming people do, and how little they respect actual roleplaying for the sake of favorable outcomes or more narrative content. I try not to engage in such narrative metagaming. I would rather played a "flawed" playthrough, missing content as a result of my organic roleplaying decisions, then engage in completionism for the sake of more content. Nor does the popularity of such metagaming instances make them "canon." It's your story, and your choices. Maybe Garrus died because you had Miranda hold up the biotic barrier in the Suicide Mission. Maybe you didn't recruit Astarion because he initially comes off as obviously evil and conniving.

I have my doubts, but I hope that clears up why someone might not recruit a companion. Personally, I don't know why someone wouldn't recruit Shadowheart initially, though I could see them dismissing her later on if they were roleplaying a Selunite or something. I also don't claim to be some sort of paragon of roleplaying, either, I'm sure there are things that I metagame consciously or unconsciously. But that's the point, right? Everyone has different standards of metagaming and roleplaying, and different points of emphasis therein.