I think I’ve mentioned this before, but it would be nice to have a button (as on the MacOs native TextEdit) to convert or permit editing in a text-only format, rather than Scrivener’s use of the Mac’s native rtf engine. That way, writing Markdown, LaTex, importing wonky files and squirreling out unwanted artifacts that appear after Compile would be so much easier. apple-convert-space??? (See my posts on the gremlin)
Don’t use rich text features, if you don’t want them. Use Paste and Match Style when pasting alien materials, and use Zap Gremlins if something is weird.
What form Scrivener uses to store your document data is unlikely to be choosable ever and should be a don’t care from the front end.
For the record, in your Gremlin thread it was determined that there was no unruly gremlin in your case. Scrivenings View mode got accidentally enabled and you did not recognize it as such.
FWIW, the vast majority of our users want more text formatting, not less. “Be more like Word” is a much much more common request than “be a Markdown editor.”
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This has indeed been brought up a few times…
- Plain Text support and syntax highlighting
- Customizable automatic Highlighting
- rich text driven “code hiliting” for markdown in editor?
- plain text
- Future wishes for MMD integration
- …
And that was just searching the wishlist tag for “syntax highlighting”.
As you will find, the main problem with this idea would be: are you willing to give up images, styles, annotations, highlighters, footnotes, cross-references both functional and personal to research, &c? Perhaps, but I don’t think most would, and it would be supremely awkward to have a majority of the menu system and a whole toolbar disabled in such a hypothetical mode.
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Not only that, but actual “gremlins” are as plain-text as it gets. 
They are physical characters, just like the tab character, or the space, or the letter “D”. Most of them herald from the days of yore, which is why they are dutifully conveyed, as part of ASCII and compatibility layers that handle ASCII, like UTF-8, even if their purpose is now lost to time (like the character that causes the system beep tone to emit). They plague coding editors just as much as anything else (and for that very reason, many coding editors will print the offending character’s code point if it wouldn’t print otherwise). In fact, we took the name “Zap Gremlins” from a plain-text editor on the Mac: BBEdit
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