It's not that hard.
Period (.) ends the sentence, comma (,) breaks up the sentence. If the next sentence is closely related, end the sentence with a semi-colon (;). For every other type of break--especially those that resemble the natural and chaotic shifts of thought we all have--use an em-dash. (Oh, and put text you want to be optionally skipped in parenthesis.)
Em-dash is probably the most natural punctuation; it best matches the kinds of shifts our brain does when thinking.
It may be due to AI proliferation, or the culturural bias I have, but I increasingly find em-dashes jarring.
As you point out, authors use them for the "natural and chaotic shifts of thought we all have" and when there are lots of these shifts it feels like I have to keep track of multiple conversations at once.
For example, in the article we have:
If your goal is to have other people read—and hopefully enjoy—your writing, you should make an effort to edit your thoughts.
When I read this I instinctively pause the 'main' thought/voice, read the aside, then re-establish my train of thought. In my opinion the sentence reads just as well without the aside:
[edit - putting comma back in to break up the long sentence] I think this is the only aside formatted like this in the article. The other em-dashes take the place of pauses in sentences, places I would normally use a comma or semicolon, or are used to introduce a list where I would typically use a colon.Again this is probably a cultural thing, maybe a reaction to AI as well, but I find the em-dash a lot more though-interrupting than the other punctuation choices and I wonder if it's something I'll get used to or not.