Multiple X11 xkb layout not supported

I am using (and since more than 3 years now) a dual Xkb configuration using the following X11 configuration:

Section "InputClass"
  Identifier "Keyboard"
  MatchIsKeyboard "on"
  Option "XkbLayout"  "fr,fr"
  Option "XkbVariant" ",bepo"
  Option "XkbOptions" "grp:shift_alt_toggle"
EndSection

Section "InputClass"
  Identifier "typematrix"
  MatchVendor "TypeMatrix.com"
  MatchProduct "USB Keyboard"
  Option "XkbLayout"  "fr"
  Option "XkbVariant" "bepo"
EndSection

On my business laptop, I can then type on the integrated keyboard using azerty, and on an external keyboard using the bépo layout. This is really handy, and is working so far in every application I used, including Gtk application and Qt application (Qt<5), such as Qt Creator, that is compiled against Qt 4.8.5.

I am currently building a small application using Qt 5.3.2 and Qt Designer. A simple combo box doesn't want to use the bepo layout, it only uses the azerty one.
If I compile the same code using Qt 4.8.5, I can use both keyboards using their own layout, as expected.

It may be a duplicate of QTBUG-40942.

I understand this is a corner case, but I see it as a regression from Qt 4.8.