Comparing the gtk2+opengl rendering to the lesstif+xrender rendering, they do the same:
(The same happens with any other group as well, silk was just an example.)
The translucency between different groups will not happen with gtk2+gdk and lesstif-without-xrender.
The simplest way to try it out is from the command line:
./pcb-rnd foo.lht -c appearance/layer_alpha=1
If you find the right value, you can put it in any of the config files the same way you did with the invis-color.
It is also possible to change it on the fly, using the following action:
conf(set, appearance/layer_alpha, 0.2)
If you are using the gtk+gl HID, it is possible t change this value from the preferences window (Config PoV tree, appearance, layer_alpha).