I’ve merged your question into a thread with a very similar discussion. I would start at the top, or jump to this post, which I’ve written as a primer on using Markdown and Scrivener, and has links branching off of it (and back-links leading to it).
Also of further interest, given some of the points in your query:
- Default Preferences to Emulate Plain-Text: I don’t waste time formatting text down to the character, and my aversion to that whole way of doing things is in large part why I write using Markdown in the first place. That Scrivener can do that can be entirely ignored.
- Specific tips and links for Zettelkasten usage in Scrivener. Note this also branches off into multiple tangential topics, and has a fair number of back-links as well that might lead you to interesting places. This of course isn’t entirely Markdown related, but since you are looking to build a knowledge system in Scrivener, I figured there might be some useful tips in there. It’s a very robust tool for this kind of work!