I use a version of what Holly described along with an additional document I call "Additional Scenes" that gets at what you are describing, I think.
Here is how it works for me:
My WIP went through two initial drafts where I was just trying to create the characters, tone, style and basic plot. That was brutal. Near the end of draft two, I finally "saw" the real plot and story and quickly wrote about 10 pages of about 40 points that defined the entire book. This came to me in one powerful "Aha" moment once I had several rough drafts. Those ten pages describes WHAT happens, WHY it happens, and HOW it moves the story--answering those questions for each of 40 or so major plot points or "events" from beginning to end.
On ANOTHER word doc I make notes of the "additional" scenes I need to add to increase emotion, character insights, subtle character development, atmosphere, whatever. These "scenes" (or microscenes) can only be a paragraph or a page, and I keep them separate from the major plot points. The second list is evolving, and I add to it each day.
Both lists are in Word on a tablet and they are the two major lists I use to focus my daily efforts, which are done on Scrivener.
So, that is my workflow as I am trying to keep it simple, while also addressing all of the points I think you raised.
Everyone creates differently. It is smooth sailing for me now, because I have some edgy and spontaneous drafts to work with.
If I had tried to plot too much too soon I think it would have become too mechanical--for me. But again, I know people work differently. That is just how I work.