Whether this problem is in xdg-utils or enlightenment_open, I don't know (but doesn't the former call the latter under E?); however, the way links are opened -- or not opened -- by E is wrong.
Apparently, E only consults ~/.local/share/applications/defaults.list -- at least, that's the case here -- while it should first consult ~/.config/mimeapps.list and then, maybe, something like ~/.config/e-mimeapps.list, according to the current standards. Let me explain the issue with an example:
A text editor -- whatever -- is the default app for opening "text/plain", as defined in ~/.config/mimeapps.list`. All Linux DEs see that but E doesn't. If I have a link to a "text/plain" in a Qt app that opens links with QDesktopServices::openUrl(), the job will be done correctly under all DEs (even under an infamous DE like gnome) except for E -- unless I add the app in question to ~/.local/share/applications/defaults.list, which would be cumbersome for all apps. Believe me when I say that only enlightenment_open opens plain texts with Wine by default here!!
I always have the latest stable E and EFL -- sometimes, I also try unstable versions. I know that E has its own ways of dealing with various things but this one is quite wrong, IMHO.