I'm confused as to why you find Obsidian not matching most those criteria. I heard about it here last week, and just installed it finally tonight, but as I understand it. It's just a bunch of markdown files in a folder on the local disk. That seems.pretty easy to access/convert, is private, is lightweight, and is future proof (I could write something in Perl to generate the graph in a night most likely).
I don't know anything about the others, since I haven't really used a note system before, so I can't comment on them. Your system seems to violate a few of your stated concerns though (is it cross compatible?), so I'm confused as to why you find it better.
there have been reports of Obsidian breaking and deleting notes when removing bidirectional links. I’m not interested in something that isn’t 100% failsafe when my notes are on the line.
That's worrying if true, but something hopefully they'll fix. I imagine deleting notes should be a fairly rare occurrence, so putting safeguards around it (such as a confirm, maybe moving note file to a trash location for later cleanup) is warranted.
Given what it is, it's probably safe and a good idea to make the vault on top of a versioned file system, even if that's a dropbox, google drive stream folder, or backblaze folder. It's probably not too hard to get a solution that's encrypted so it's more private as well.
I still think replacing the document creation markdown handling with Obsidian, which also shows back-links and lets you easily follow links, is probably much more useful and efficient than to use a regular text editor and manually curate the folders and tagging.
You probably want versioning in all cases (your manual method or Obsidian), and it doesn't negate the benefit of a system that scans and builds a graph of your knowledge provides.
I don't know anything about the others, since I haven't really used a note system before, so I can't comment on them. Your system seems to violate a few of your stated concerns though (is it cross compatible?), so I'm confused as to why you find it better.