The answer to your question 1 is essentially laziness and the inability of the refactor plugin to “update links to headings.”
I understand the value of having each quote + annotation broken out into individual notes, but then I’d have to actually name all of them (I did in the example but I don’t always, it’s extra work that is often unnecessary), and contrary to most principals of “what should go into a pkm vault” I’ve read, I actually think it’s an enormous waste of my time to re-word everything I read before letting it have a home in my notes. I understand the value of rewording things in order to ensure one’s own comprehension — I am a teacher, after all — and I understand the dangers of “raw capture” instead of “recording your own knowledge” but most of my litnote+annotation workflow is with sources I have only temporary access to, are comprised of information I’m not so much “trying to understand” as “trying to make sure I don’t forget the details of,” so in that case, having the actual quotation (plus my annotation about why it’s important and what it’s for and what it means) is the important part. From a workflow perspective, that means that most of my litnote is exported from something like Readwise or an annotated pdf’s highlights, and going through and refactoring it it often more trouble than it’s worth (but having it searchable in my “database of knowledge” is invaluable).
If I were a student using my vault to record learning I would absolutely have a different approach, but since I’m not, forcing everything to be artificially atomic makes it harder to do things like write a book review or review the “flow” of the important parts of a particular book. And usually I remember where I read something (“Didn’t The Horse, The Wheel, and Language say something about cattle, too?” might wind up relating to a section that would not reasonably have had a title about cattle, horses, wheels, or language 
and while I could use a source note, that adds an unnecessary step that feels like added friction) but not what the rest of the surrounding context of the data point was.
the tl;dr on that is that I totally agree with you about the dangers of the whole “tight coupling” thing but in the end I decided not to let the perfect be the enemy of the good and that saving time by minimizing extra steps was more important than having the optimally atomic layout, given my particular goals.
The answer to your question 2 is also efficiency. Why do the same work twice? Once I’ve had a particular thought, I don’t need a note that says the same thing. I’m not going to transclude my evergreen atomic note into another source, I’m going to say “This relates to [[article]] where I said thing.” Being able to do "This relates to [[article]] where I said [[thing]]" doesn’t really gain me much, and means that if I search for [[thing]] I’m going to get two results, which makes my results harder to trawl for useful information, not easier.
I almost always never write evergreen notes for the sake of writing notes. I don’t take notes “just to have them.” I take notes because I plan to use them, and thus far I haven’t hit a point where I’ve been like "gee, I should develop my thinking on topic" that hasn’t resulted in something I want to share with the world. If I notice a connection like “Suttee, Sacral Kingship, and Human Sacrifice are related in ways that haven’t been explored by any academics I’ve seen,” I’m not going to make an evergreen note about suttee, sacral kingship, and human sacrifice and then go write an article about it. I’m just going to write an article about it. Maybe I’ll create MOCs about suttee, sacral kingship, and/or human sacrifice that point to various notes I’ve taken on the subject, but the way my brain works, creating an evergreen note for each and then synthesizing them later is just unnecessary work, and I’m pathologically opposed to unnecessary work.
Basically, I only do as much work as necessary to facilitate my goals — and I think our goals are different. But maybe I’ll shift over to a more atomic-evergreen-note centric focus as I grow my vault. I’ve made other shifts and adaptations over the months!