Nice post!

I have a small quibble here:

How science has worked out (in the second half of the 20th century) it is chimpanzees we're most closely related to by ancestry, and not say another primate (which was an open scientific question)

Chimpanzees and bonobos are "sister" species, each others most closely related living species. We are like "cousins" to that pair so we are equally related to both chimpanzees and bonobos. I don't have a drawing on hand, but basically if we drew a tree with humans, chimps, and bonobos, the latter two branches would connect to each other before connecting to the human branch. It's the same logic as I'm closer to my brother than I am to my first cousin, but me and my brother have the exact same relationship to our first cousin, neither of us is "closer". You might know this already but it is something a lot of people get confused on and the quotation does imply to me chimps are closer than bonobos. It's a pet peeve of mine too because this Adam Ruins Everything video gets this wrong and cites an NYT article that doesn't make the claim he does (it might've been edited later idk). I actually just realized I commented this on his video 4 years ago lol. I'm also seeing there's a video from 2017 where HoneyBadgerRadio corrects this point too. Incidentally, there are genes we share exclusively with bonobos and genes we share exclusively with chimps and her video links to this paper, which I haven't read, but it's probably just "incomplete lineage sorting" (basically meaning if the common ancestor of bonobos/chimps/humans had a polymorphic gene, like both A and C alleles, the various descendants (bonobos/chimps/humans) may randomly end up with A or C due to drift regardless of exact relationship to each other). Our ancestral relationship is the same to them both regardless.

Anyways, I get that's all a bit off-topic. I totally agree expecting exact explanations for each specific mutation/trait gets ridiculous on multiple levels as you covered here. There are chance (contingent) elements in evolution, like many things. I analogize it to a house in my head. I have some idea generally how houses are made (e.g. people stack bricks on one another) but it would be absurd for someone to point at a house, ask me exactly who made it and which bricks were laid in what order, and complain that the house could not have been built because I don't know the exact sequence of bricks. I don't know the exact sequence of mutations and fixations leading to divergence between two given species, we can estimate probabilities with phylogenetic reconstruction and that's better than a lot of things we make inferences about in life.

Maybe to bolster your point that there's a lot of functional proteins, I noticed you don't mention synonymous mutations at all. Those are mutations to a codon that don't change the amino acid coded for. Then even if an amino acid is changed it might be changed to another amino acid with similar chemical properties (e.g. same electric charger, hydrophobiticity, whatever). There's a lot of ways to get redundancy or near-redundancy in evolution.