Why is use Scrivener, is I need a tool where I can easily move sections and subsections around and give each a status/flag. There some other things in Scrivener that are nice, but this is core to me. Any other editor for writing books where I can easily see and move sections around is not for me.
Didn't you mean to say "where I _can't_ easily see and move things around"? or are you making a different point I'm not understanding, because it looks like you're negating yourself and I'm not sure what you mean.
One poor man's highland is putting together the requisite functions in VSCode or Atom. Neither currently has an add-on with the ability to move sections of .md, but if someone adds this, it would be a huge contribution to the writer community.
