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I finally discovered why stencil operations (ground primitives and silhouettes) were not working on my machine. Normally the globe depth fbo is the principal fbo for the scene, but when the depth texture extension is not supported the FXAA fbo is used. I needed to change the FXAA depth texture/renderbuffer to use depth-stencil instead.
This also explains how we got away with not passing in
stencil : true
to the WebGL context. Even if the default FBO is not initialized that way you can still create FBOs with stencil buffers. So when I turned off depth textures and fxaa, so as to use the default FBO, the ground primitives were in fact broken. I just copied some of the code from #4314 into here to deal with that.