When creating a 2D Style, and using the Evaluations to create the color,
shape, fill, etc, is there a way to generate the code such that the fill
for a rectangle does not automatically subtract from the width and height
(thus forcing an outline)? This may also happen with other shapes but I have
not experimented with those yet.

It should be fill completely though that can be implementation specific -- for exam ple Repast has a mode where gird lines are always visible. I'll look into it for Ascape target. I am als planning to add a relative size constraint per an earlier suggestion.

When working with a style, just evaulate to a red, rectable, fill, and you
will see the generated code subtracts from width and height. I have to manually
change the style to get it to fill completely.