Q:

URL protocol handlers in basic Ubuntu Desktop

There was a way to register URL protocol handlers with Gconf, which is now obsolete and there seems to be no way to do the same with DConf (or Gsettings, its recommended wrapper).
How do one properly register an URL protocol handlers since DConf?
Additionally, something looks strange to me (as I don't understand it), on my Ubuntu 12.04
The protocol apt:// should be handled by the apturl command. It is so with my Opera browser, but only because I added this specific association using the browser's configuration facility. Otherwise, in the rest of the environment:

Running xdg-open apt://foo.bar opens elinks (my www-browser alternative).
Running gnome-open apt://foo.bar opens the Software Center.
Opening gconf-editor, I see a key /desktop/gnome/url-handlers/apt whose value is apturl "%s" and it's enabled. This configuration seems to be ignored, which is reasonably expected, as GConf is considered obsolete.
Opening dconf-editor, I can't see anything related to URL handlers or protocols in /desktop/gnome

It looks a bit messy to my eyes (just teasing with this wording, nothing bad)
What's underneath?
Side note: I'm looking for something which preferably works even when the full desktop environment is not loaded, like when running an i3wm session with only gsettings-daemon (and other stuff unrelated to this case) loaded.
Update
Another way to “register” a protocol handler is with *.desktop files and their MIME-Type; e.g. MimeType=application/<the-protocol>;.
I found a /usr/share/applications/ubuntu-software-center.desktop with this content:
[Desktop Entry]
Name=Ubuntu Software Center
GenericName=Software Center
Comment=Lets you choose from thousands of applications available for Ubuntu
Exec=/usr/bin/software-center %u
Icon=softwarecenter
Terminal=false
Type=Application
Categories=PackageManager;GTK;System;Settings;
MimeType=application/x-deb;application/x-debian-package;x-scheme-handler/apt;
StartupNotify=true
X-Ubuntu-Gettext-Domain=software-center
Keywords=Sources;PPA;Install;Uninstall;Remove;Purchase;Catalogue;Store;

This one explains why gnome-open apt://foo.bar opens the Software Center instead of apturl.
So I installed this apturl.desktop in ~/.local/share/applications:
[Desktop Entry]
Encoding=UTF-8
Version=1.0
Type=Application
Terminal=false
Exec=/usr/bin/apturl %u
Name=APT‑URL
Comment=APT‑URL handler
Icon=
Categories=Application;Network;
MimeType=x-scheme-handler/apt;

After update-desktop-database and even after rebooting, both xdg-open and gnome-open still do the same and ignore this user desktop file, which as usual with user desktop‑files, should override the one in /usr/share/applications/.
Maybe there is something special with desktop files specifying x-scheme-handler MIME type and they are not handled the usual way.
The desktop‑file way does not answer the question.

A:

Open ~/.local/share/applications/mimeapps.list and add a line like:
x-scheme-handler/apt=apturl.desktop

A:

xdg-mime
Maybe more elegant (in this example I use "apt", change it for any other scheme):

Check registered MIME-types in /usr/share/applications/defaults.list.
Add the apt.desktop file (here some examples) to ~/.local/share/applications/ (user-wide) or /usr/share/applications/ (system-wide).
Build cache database of MIME types handled by desktop files: update-desktop-database
Register a protocol with
xdg-mime default apt.desktop x-scheme-handler/apt`

This will append the new MIME Type for the scheme to ~/.local/share/applications/mimeapps.list. You can register the new mime-type for all users on the system sudo xdg-mime install --mode system <xml file>.

Test with xdg-open "apt://foo.bar".
See also Adding a MIME Type.

