@Ikuya: I found that gnome-settings-daemon 3.18, which is in the Xenial
archive, also overrides those two variables. So my guess is that you had
3.20 on your Xenial installation. (If not, this is still a mystery.)

Anyway, I prepared merge proposals for gnome-session (Yakkety and
Xenial), and attached a Xenial patch for gnome-settings-daemon.

** Patch added: "gnome-settings-daemon_no-im-override.patch"
   
https://bugs.launchpad.net/ubuntu/+source/gnome-settings-daemon/+bug/1594681/+attachment/4720456/+files/gnome-settings-daemon_no-im-override.patch

** Description changed:

- Currently these variable settings are hardcoded in gnome-session:
+ [Impact]
+ 
+ Currently these variable settings are hardcoded in gnome-session and
+ gnome-settings-daemon:
  
  QT_IM_MODULE=ibus
  XMODIFIERS=@im=ibus
  
  That way the use of alternative IM frameworks, for instance fcitx, is
- prevented. gnome-session should drop those variable assignments, and
- rely on im-config instead.
+ prevented. The variables should only be set if they are empty, so the
+ values set by im-config are honored.
+ 
+ [Test Case]
+ 
+ * Install Ubuntu GNOME
+ * Install fcitx
+ * Set fcitx as the input method:
+   im-config -n fcitx
+ * Relogin
+ * Check the IM-related environment variables:
+   env | grep -E '_IM|XMOD'
+ 
+ After the proposed uploads of gnome-session and gnome-settings-daemon,
+ those variables are consistently (unlike before) set to "fcitx".
+ 
+ [Regression Potential]
+ 
+ Low. im-config sets "ibus" by default in Ubuntu GNOME anyway. This
+ change prevents an inconsistent input method configuration for users who
+ have actively chosen some other IM framework.

-- 
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https://bugs.launchpad.net/bugs/1594681

Title:
  Don't override IM variables

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