this only partially addresses your complaint, but you may or may not be aware that markdown has an option to put urls in footnotes, which you can put anywhere in the file:
(This is part of the background work for [Monnier’s paper with him
about Elisp’s history][3] for HOPL ’20.)
...
[3]: https://dl.acm.org/doi/pdf/10.1145/3386324 (Evolution of Emacs Lisp, by Stefan Monnier and Michael Sperber)
in my .emacs.d/init.el i wrote a command https://github.com/kragen/kragen-.emacs.d/blob/master/init.e... which inserts such a footnote link, linking the previous word to the link pasted from the clipboard. it auto-increments the footnote counter, initially setting it higher than any numbered footnote it finds in the file. i have it bound to the fairly horrible key ctrl-alt-]; successive presses of the key expand the link leftwards to include more words
(it ought to use the selection as the link text if there is one, and to find an existing block of footnotes to add the footnote to if there is one, but i haven't implemented those features)
the upshot of this is that in the above, after typing 'history', i pressed ctrl-alt-] and kept pressing ] until the link had engulfed monnier's name
emacs markdown-mode does also automatically syntax-highlight links, headers, bulleted lists, italic, bold, typewriter code, and markdown linebreaks, and it has a command (the also rather horrible keybinding ctrl-c ctrl-o) to open a link. if the link is to a local file, it opens it in emacs rather than your browser. it also uses the tab key to expand and collapse headers, and of course it always has emacs's instantaneous full-text search. but the formatting is much uglier than obsidian's
(it ought to use the selection as the link text if there is one, and to find an existing block of footnotes to add the footnote to if there is one, but i haven't implemented those features)
the upshot of this is that in the above, after typing 'history', i pressed ctrl-alt-] and kept pressing ] until the link had engulfed monnier's name
emacs markdown-mode does also automatically syntax-highlight links, headers, bulleted lists, italic, bold, typewriter code, and markdown linebreaks, and it has a command (the also rather horrible keybinding ctrl-c ctrl-o) to open a link. if the link is to a local file, it opens it in emacs rather than your browser. it also uses the tab key to expand and collapse headers, and of course it always has emacs's instantaneous full-text search. but the formatting is much uglier than obsidian's