Zettlr converts HTML to markdown using the Showdown library iirc (I don’t know what Obsidian uses), so I’d hope it would be a reasonable comparison with Obsidian.
I certainly don’t see it as simple and personally prefer to paste without formatting when I hit a problem between programs - trying to work out whether it’s a problem with clipboard, target or translation can become unproductive very quickly. I doubt it’s a bug in Obsidian itself, which is the original claim. The problem is likely to be somewhere upstream, and if no-one has spotted what it is by examining the clipboard content then the only way forward I see is testing for the boundaries of problem occurrence. The OP started, but it seems to need to become much finer grained.
I’m a bit surprised that other Apple Notes users haven’t reported similar issues, but don’t remember seeing them.