Hey,
I rebooted the VM after adding your line to rc.local, and indeed it
fires up. I'm assuming that rc.local runs before X server starts up.
The command I want to run is 'setxkbmap'.
Either way, I looked at the link you've posted and it made me think to
look inside /etc, where I found:
(fedora-26) /etc/X11/xinit/xinitrc.d/qubes-keymap.sh
(debian-9) /etc/X11/Xsession.d/90qubes-keyboard
From my understanding it is a script that runs automatically at X server
start up, which parses the user's keyboard settings in
~/.config/qubes-keyboard-layout.rc.
The only problem was that it parses only -layout and -variant but not
-option, so I've added that capability to the script (attached), thus
allowing it to add custom key combinations for layout switching.
Then I added the necessary options in
~/.config/qubes-keyboard-layout.rc, each separated by a + sign:
us,il,ru + ,,phonetic + grp:alt_shift_toggle
And that worked perfectly for me.
Then, after another thought, since I want the same layout configuration
to propagate to all the VMs, I just commented out the entire script, and
added the command I wanted in the end (last line in the attached file).
That worked perfectly well too.
Solved!
Thank you for your help.
--
NaBaCo.
PS: If relevant, I'll be glad to make a PR for the script and to add
this into the official documentation.