Good post .. I have been researching editing and publication tools for markdown based ebooks. I will look into scrivener, but so far, most markdown editors produce one pdf per .md file, not for a directory of files - do you know of any.
And yes, ST2 is fast, and easy for Markdown editing, but I dont really use any plugins, etc.
Well I just name the files 00 Frontmatter.md, 01 Chapter 1 xyz.md, 02 Chapter 2.md, etc.
I find this ordering helps me mentally organize thoughts in writing markdown ebooks.
Then on windows I do a "dir /b/A-d/On >> fileslist" to get a list, that I feed to a ebook generator to get .pdf, .mobi, .epub, .epub3, etc. files from markdown and pandoc.
There is a manual step in connecting the list of files to proper Chapter titles, but am working on script tool for extracting first line of each markdown file.