@f2thak
Have you managed to get Theme Customizer support "Show app shortcut backgrounds"? I saw a previous post of yours and i was wondering why you were having that problem and I didn't.
Yesterday I updated Theme Customizer to the one in the devel repo and lost the option to make icon backgrounds transparent so I uninstalled it and installed the one in extras instead. I got the option back, maybe you should give it a shot if you haven't fixed your problem.