Considering that one of your requirements is already using .md files, which is a format pretty common… maybe a combination of different apps on different platforms would work? Specially considering that mobile UIs are likely gonna have different requirements than desktop UIs.

One approach I was considering was using neutrinote on Android (which is a relatively simple but functional no-bullshit markdown editor supporting cross-linking between markdown files) and VSCode / VSCodium on the desktop (which also supports cross-linking, and I think has some note-taking related extensions), or maybe zed, or whichever editor you might already be using that can support markdown. Then use syncthing for the sync.

However, I have not yet really gotten into it, primarily because second brain/zettelkasten note-taking in general has never really fully clicked with me, most of the time when I take notes I just use them as a scratchpad / temporary storage… without much of a proper organization … just a note meant to be scrapped as soon as it’s acted on. Often I just use tabs in my notepad app, without really saving them to a file.