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You're actually bringing a bunch of different topics together with the TOC vs. paragraph discussion. Best to keep focus on one issue at a time.
For starters - did Auto/Auto on the paragraph type and formatting not work in terms of file generation (forget about the TOC)?
I think I can see a potential issue, please confirm if I'm right. You are basically using 'pseudo' markdown formatting - based on your example you're not using spacing between paragraphs. 'Official' markdown formatting requires a blank line between every paragraph. Basically markdown 'requires' block formatting.
Putting a space between every paragraph will make it block formatting which is what you've discovered. It doesn't actually matter that you set the style to single, the fact of the matter is that the markdown engine gets called, and it requires block.
I think the older rev of the input plugin let you combine the two, but the recent changes don't allow that.
I can see an argument though for allowing 'single' style formatting and markdown text. It wouldn't be hard to modify text input to support that, especially since the plugin modifications make both configurable.
Regarding the TOC, I'm not really sure what the problem was there... I didn't think auto-generated would make any difference for text input.
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