I'm on Arch Linux with xdg-utils 1.1.2.
Opening a magnet link with xdg-open will open that link in the default bittorrent application.
Opening a magnet link with xdg-open opens the link with the browser. Probably not the same as bug 96472, in my case $BROWSER variable is not set and xdg-mime query comes back empty.
Steps to reproduce:
1. Set the default handler for magnet links: xdg-mime default rtm.desktop x-scheme-handler/magnet
1a. Check if 1 was set succesfully:
$ cat ~/.config/mimeapps.list
1b. Make sure that $BROWSER is not set:
$ echo $BROWSER
2. xdg-mime query is coming back up empty:
$ xdg-mime query default x-scheme-handler/magnet
3. Run `xdg-open magnet:?xt=foo`.
4. The magnet link will be opened by the browser instead of the default application for magnet links.
Various blog posts suggested that the issue *might* be due to the xdg-open not recognising DE properly - sadly, my shell-fu is not up to the task to asses it. For what it's worth, I'm using a tiling wm instead of full-blown DE.