First up, we’re on the same page. Recovering from disaster is too often a forgotten priority, and I agree plain text is wonderful stuff.
You offer great food for thought and it occurs to me there should be points of cooperation between output format and software.
The manipulations you mention should all be easy in a proper word processor, and I would not want to use any such application without being able to recover documents without using the app.
That’s one of the things I like about Devonthink. I might lose organization but I can always snatch my documents out of a Devonthink database.
That’s never been needed, of course.