As Dr. Drib mentioned, Scrivener does have an automated backup function which can be customized to make a copy with each manual save, which may or may not help with the learning.
And the file format is basically a bunch of readily-readable open ones (odt, rtf, xml, etc.) within a package wrapper, which
Marked2 can read, and
Storyist can import and export. Though admittedly that's pretty limited direct support for working with .scriv bundles as-is and I can see how that could be a concern.
As for incorporating research sources, it seems like you've a pretty good setup via Calibre already and wouldn't benefit at all from using the built-in. (Which personally, I don't bother with since I don't like the way the document viewer shows stuff, so for extra note purposes, I just make text files with file:// links to the relevant folders so I can pick whichever external app to open with.)
But yeah, it does sound like Scrivener is unfortunately not suited to your workflow.
It's really too bad the potentially useful-looking plugin extensions for OpenOffice don't seem to be kept up to date, since this one for
Author Support Tools looked pretty promising, with an element outliner for existing documents, and notes tools, and reference management. The
LibreOffice extensions listings don't seem to have anything like it (though they've a pretty cool-looking ODT to Braille converter).