This seems reasonable to me if the base system is modified to let "safe"
commands through as you suggest.

> So, I think that what's needed on the LaTeX side is for epstopdf's
> functionality to be incorporated into graphics.dtx.

Wouldn't this would go in pdftex.def which is no longer part of the
core latex/graphics system so it can more easily track pdftex features?
%% The Current Maintainer of this work is
%% Heiko Oberdiek and Martin Schr\"oder.

Actually wouldn't it be enugh to simply say something like 
\ifpdf \RequirePackage{epstopdf}...
in the graphics.cfg distributed with tex-live or other systems that have
write18 turned on by default?


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