This issue encompasses a few things. First, we need a printout which shows the different culling bits, opaque regions, render roots, etc. This helps to determine why things are being rendered, etc. Example:

*=Render Root
d=Dirty
dt=Dirty By Translation
i=Dirty Region Intersects the NGNode
c=Dirty Region Contains the NGNode
ef=Effect Filter
cf=Cache Filter
cl=This node is a clip node
b=Blend mode is set
or=Opaque Region
ensemble.EnsembleApp$1 [*0 *1 i0 ci1 or=0.0, 0.0, 1024.0, 768.0]
  PageBrowser [i0 ci1]
    HomePage id=HomePage [i0 ci1 or=0.0, 44.0, 1024.0, 724.0]
      VirtualFlow id=virtual-flow [i0 ci1]
  MenuBar [or=0.0, 0.0, 1024.0, 0.0]
    HBox

Second, we should fix the showDirtyRegions so that it doesn't render the entire scene every time

Third, we should add a mode to draw overdraw rectangles to indicate how many times a specific part of the scene has been drawn. Ultimately we'd want this to be pixel perfect and completely accurate (basically we should record every time any pixel shader touches a specific pixel), but for now a simple rectangle based approximation will work.