I try to render using GLSurfaceView, and by docs I set format:
getHolder().setFormat(PixelFormat.TRANSLUCENT);
The I use GLSurfaceView.Rend
OK, after some research I can answer this myself.
I finally made it to be drawn with transparency using SurfaceView.setZOrderOnTop(true). But then I lost possibility to place other views on top of my GLSurfaceView.
I ended with two possible results:
On left is standard GL surface below all other views, which can't be drawn with transparency, because GL surface is drawn before application's window surface, and GLSurfaceView just punches hole in its location so that GL surface is seen through.
On right is transparent GL surface drawn with setZOrderOnTop(true), thus its surface is drawn on top of application window. Now it's transparent, but is drawn on top of other views placed on it in view hierarchy.
So it seems that application has one window with surface for its view hierarchy, and SurfaceView has own surface for GL, which may be on top or below of app window. Unfortunately, transparent GL view can't be ordered correctly inside view hierarchy with other views on top of it.