It mostly has to do with how rich text, all by itself, isn’t something easily converted to something that is not about formatting at all, but rather declaring intention, or semantics, to the text. With Markdown it is extremely clear that if you put a > in front of a paragraph, it will be a block quote. But that is not so clear at all in the case of rich text, with there being an indent, and maybe a different spacing style, etc. But that could also be something else, maybe an epigraph, and there are a million and one ways to format a block quote. So how is an algorithm to guess what you meant from the raw RTF formatting?
That’s where styles come in, because styles also declare intention, and we can do things with them in a functional sense, like go into the compile settings and tell “Quotation” styled text to be prefixed with > on each line (or better yet, in the Markdown Options compile format pane, bind that style to the block quote generator).
Converting to style-based text isn’t too difficult, if that’s your concern. The Edit ▸ Select ▸ Select Similar Formatting tool can go a long ways as that will select all matching ranges of text at once, which you can then apply a prepared style to. In this way you can “train” the compiler what such and such an amount of indent, or paragraph spacing, means to you.
I may be a little confused though, because you say you want to integrate with Obsidian, which is a 100% pure Markdown writing environment, but then also say you want to compile from Markdown—and the initial thing you were trying to use is a tool that would remove Markdown and convert it to rich text, which Obsidian won’t have a clue what to do with.
So going off of at least the one part that is clear to me—integrating with a Markdown editor—what you do probably want then is to set your Compile For drop-down to plain “MultiMarkdown” (so you get an .md file), select “Basic MultiMarkdown” as your compile Format, and then for the Section Layouts, set up which parts of your binder outline should print headings and/or text.
At that point you’ll want to customise the Basic MultiMarkdown format a little bit for line breaks because it sounds like you have word processing paragraphs instead of Markdown paragraphs in the editor. That’s an easy fix, as the format is already set up, it just needs a couple of checkboxes enabled to turn it on.
After that, I can’t really provide specific advice, because the rest is what I referred to earlier as “training” the compiler. I would compile initially with what you’ve done so far, and then start going through the original and looking for meaningful rich text that isn’t converting to Markdown and getting things working with styles. Again check the available styles already in that format, and in the Markdown Options tab, both may save you some time on setting up that part of it anyway.
One thing I can recommend is something I do: have a “Stylesheet” document in your binder. Select that, and use the “Current Selection” compile group setting so that is the only thing that compiles. The idea here is to copy and paste the different rich text samples you have into this file, style them, and test the compiler settings against them. Compiling a one or two page sample like this will greatly speed up the experimentation process.
The good news is that once you do this, you’ll be well on your way to have your own personal writing setup that works the way you want.
Turns out markdown interpretation extends to requiring space separated paragraphs if you switch on markdown for compilation too.