Running the game on Xorg set up for 10bpc/30bpp color makes the window appear transparent.

 To enable 10 bit color, I use a conf file in /etc/X11/xorg.conf.d that looks like this:

Section "Screen"
  Identifier "Default Screen"
  DefaultDepth 30
  SubSection "Display"
    Depth 30
  EndSubSection
EndSection

Disabling 10bpc color by commenting out this entire Section and rebooting (to restart X) makes the game look normal. This is what happens on both Gnome and a fresh Cinnamon install.
The issue seems to be similar to MC-134586, but specifically arises with 10 bit color.