Perhaps another 0.01 CAD worth, to add to the other one I threw in earlier.
Meanwhile I'll remind you of what I said earlier. If you are going to have two levels of abstraction - regardless of how close or far they are from each other - you need to have two presentations within your model.
You mention that prefixes should not be visible in the model. However, you want clear, readable code. I will stick my neck out here and guess that you also want the code to compile as you specify.
I am going to stay well away from the methodology stuff here. I do strongly agree with what is being said there, but you are in the middle of something, and research, selection, adoption, and implementation of a methodology might, within the scope of your current project, negatively affect your critical path.
If you want some portion of your model to accurately map to the code you will need, at least in this model portion, to have the prefixes, or whatever, show up in the model.
[b[If[/b] you want some portion of the model to allow (some of) your audience to review the 'pure' structure without adornments, you will need, at least in support of this model portion, to conceive a mapping between the 'pure' structure and what is in the portion of the model that directly reflects the physical system.
That mapping can be realized in a transform. In your case it, as you describe your needs, this would seem to be very limited in scope and complexity. If the overall size of your model is not too tiny, then this could well pay off immediately, since you can keep the two portions in synch, and may even be able to model one 'side' and generate the other through the transform. If your model is small, then this step will probably be quite quick, and could fit within your schedule - possibly offset by reduced time needed for hair-pulling.
You could even model the components of the transformation itself, giving you a way to examine your 'in-house standards' as well as publishing the expected results, audiences, and benefits. Who knows, your various communities might actually come up with a set they could all work with...
David