Comment 18 for bug 513133
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0e1f616
(Get the code!)
Lei Zhang, I agree it's not a requirement, but as you say it is a convention in GNOME to use basenames. For example, all the other existing preferred apps use it. So xdg-setting trying to set or get any of them would fail [1].
The current behavior was suited for chromium because the script comes from chromium, but it's not a good fit for the rest of GNOME.
The issue you bring up with versions in non-standard locations could be solved with PATH adjustments.
[1] xdg-setting check default-web-browser epiphany.desktop will check for '/usr/bin/epiphany' when it will find 'epiphany' and say 'no'. And setting it will result in a 'Custom' preferred app instead of the existing option 'Epiphany'.