The full screen renderer feature is built to work with the full screen shadergraph target. The shadergraph target exposes settings for stencil but these have no affect when used with the renderer feature. 

Steps to repro:
# open attached project

Expected: The image effect (drawing green to the screen) only writes to pixels covered by the cubes.

Actual: The entire screen is green

The repro project explained:

All cubes are on the "test" layer, all spheres are on the "default" layer.

In the renderer the "test" layer is drawn using "draw objects" writing a value of 1 into the stencil buffer.

The full screen renderer feature is executed after render objects using the "FullscreenStencilTest" material.

The shadergraph for the "FullscreenStencilTest" is configured with a Ref 1, Comp Equal  stencil setting and should therefore only show on pixels occupied by the "test" layer geometry.