Ian, if I'm reading you right, what you want is to produce 2 images - a
top view and a bottom view, each view showing the combination of board,
copper, mask, silk and holes from bottom up in that order. 

Like this for example (bottom layer, mirrored, of course you can
de-mirror it post-process). 

http://imgur.com/2PWuexd 

If that's the ticket, what you need to do then is to invert the mask
layer so it's foreground is the mask "ink" itself (in order that an
alpha can be set on it) and then use them all at once, luckily inverting
a gerber is easy it seems, just stick "%IPNEG*% at the top (and probably
remove any %IPPOS*% commands already in it). At least it works for my
gerber generated from DipTrace 

Here's a quick hack job bash script to do the job, I used this script to
generate the image above... 

https://gist.github.com/sleemanj/c0db735afe029c3a478b 

Usage: 

 dirtyimager.sh Through.txt TopSilk.gto TopMask.gts Top.gtl 

filenames are obvious I hope, output gets dumped in /tmp/dirtyoutput.png


Fiddle with colours in the script to your desire :-) 

 
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