Yes, I find Time Machine pretty much hopeless. There is, however, a nice little utility available on the Mac App Store called Exporter. It will export your notes to a number of different formats (including markdown). Well worth a look, although it doesn’t appear to have been updated for a couple of years. Website: http://falcon.star-lord.me/exporter/

Various mobile (iOS) utilities – such as iMazing – also enable you to create backups of your notes (from your iPhone).

LateForDinner wrote:

I don't know if this is new, or if it has been discussed and I missed
it, but Apple Notes now has folding. You can collapse headings and
subheadings. I haven't tested titles.

Now, if only there were a reliable way to back it up. I have run tests
with Time Machine and found it less than trust worthy.