many apps(firefox for example) load their panel icon not from my configured icon theme other apps(gmplayer for example) have broken panel icons
The devel panel will have a gtkrc style property for controlling the translucency of minimized icons, if you set its value to 0, the icon will completely hide.
Devel branch has been merged in master. A 4.7.0 release will follow soon. If you think this bug is not fixed? Feel free to reopen the bug.