hotkeys do not work when xkbmap uses a regional layout instead of en_US, gnome input source is ignored

Symptom: hotkeys do not work at all. It seems to only affect letters themselves while Ctrl, Shift or Alt are interpreted (as shown in a bar at the bottom of the UI).

➜ ~ echo $XDG_SESSION_DESKTOP
ubuntu-xorg

I do have two keyboard layouts enabled, however, I used en_US in Gnome while trying to trigger any hotkey actions.

# the first one is the one used currently as this is an MRU list
➜ ~ gsettings get org.gnome.desktop.input-sources mru-sources
[('xkb', 'us'), ('xkb', 'ru')]

The default Inkscape hotkey file is used, so, for example, undo should work just fine but it doesn't:
/usr/share/inkscape/keys/default.xml
...
  <bind key="z" modifiers="Ctrl" action="EditUndo" display="true" />
  <bind key="Z" modifiers="Ctrl" action="EditUndo" />

I sniffed around little bit and found out that XKB layout was set to 'ru':

➜ ~ setxkbmap -query

rules: evdev
model: pc105
layout: ru,us,us
variant: ,,
options: grp:alt_shift_toggle,grp_led:scroll

After changing that to 'us' via setxkbmap shortcuts immediately started to work (without inkscape restart):

➜ ~ sudo setxkbmap -option grp:alt_shift_toggle us
➜ ~ setxkbmap -query

rules: evdev
model: pc105
layout: us
options: grp:alt_shift_toggle,grp_led:scroll

Doing this via CLI, however, somehow breaks switching language in gnome itself (changes are present in the MRU list but input is localized and is not switched).

The only suspicious message I found in syslog after that was this:

Dec 18 21:42:34 blade /usr/lib/gdm3/gdm-x-session[8236]: The XKEYBOARD keymap compiler (xkbcomp) reports:
Dec 18 21:42:34 blade /usr/lib/gdm3/gdm-x-session[8236]: > Error: Can't find file "<D0><D1>" for symbols include
Dec 18 21:42:34 blade /usr/lib/gdm3/gdm-x-session[8236]: > Exiting
Dec 18 21:42:34 blade /usr/lib/gdm3/gdm-x-session[8236]: > Abandoning symbols file "default"
Dec 18 21:42:34 blade /usr/lib/gdm3/gdm-x-session[8236]: Errors from xkbcomp are not fatal to the X server
Dec 18 21:42:34 blade /usr/lib/gdm3/gdm-x-session[8236]: (EE) Error loading keymap /tmp/server-1.xkm
Dec 18 21:42:37 blade /usr/lib/gdm3/gdm-x-session[8236]: The XKEYBOARD keymap compiler (xkbcomp) reports:
Dec 18 21:42:37 blade /usr/lib/gdm3/gdm-x-session[8236]: > Error: Can't find file "<D0><D1>" for symbols include
Dec 18 21:42:37 blade /usr/lib/gdm3/gdm-x-session[8236]: > Exiting
Dec 18 21:42:37 blade /usr/lib/gdm3/gdm-x-session[8236]: > Abandoning symbols file "default"
Dec 18 21:42:37 blade /usr/lib/gdm3/gdm-x-session[8236]: Errors from xkbcomp are not fatal to the X server
Dec 18 21:42:37 blade /usr/lib/gdm3/gdm-x-session[8236]: (EE) Error loading keymap /tmp/server-1.xkm

ProblemType: Bug
DistroRelease: Ubuntu 17.10
Package: inkscape 0.92.2-1build1
ProcVersionSignature: Ubuntu 4.13.0-19.22-generic 4.13.13
Uname: Linux 4.13.0-19-generic x86_64
NonfreeKernelModules: nvidia_uvm nvidia_drm nvidia_modeset nvidia
ApportVersion: 2.20.7-0ubuntu3.6
Architecture: amd64
CurrentDesktop: ubuntu:GNOME
Date: Mon Dec 18 21:24:39 2017
InstallationDate: Installed on 2017-02-27 (294 days ago)
InstallationMedia: Ubuntu 17.04 "Zesty Zapus" - Alpha amd64 (20170227)
SourcePackage: inkscape
UpgradeStatus: Upgraded to artful on 2017-09-13 (95 days ago)