If I run skypeforlinux on openbox or lxde I get some crappy tray icon:
But if I run env XDG_CURRENT_DESKTOP=Unity skypeforlinux everything works fine.
So let`s write a simple script called skype and forget about this bug:
$ cat /usr/local/bin/skype
#!/bin/bash
env XDG_CURRENT_DESKTOP=Unity skypeforlinux