I'm confused on the difference between a theoretical construct and a theory.
I apologize if anyone else has mentioned this, but I think most working scientists are uncomfortable with purely computational work and "theories" because they don't appear to be falsifiable within the framework developed by Popper. Current global climate models (GCM) are only subject to verifiability and this relegates them to a lower status then, say, Maxwell's equations. Maxwell's equations are capable of being used to explain almost all macroscopic electrodynamic phenomena, at least within the confines of classical physics. OTOH, there is no proper theory of the climate than can be treated with equal footing. There are only computational models and input data. There is a large amount of parameterization and data treatment (cynics would say massaging) that need to be done to get the models to converge.
Theories make predictions about the world. I'd argue they're useless without this. As such, they are function of a prior state, returning the new state.
Certainly you can't validate your theory without doing physical experiments, or at least having lots of data that the theory was not based on, to check it. But validation of a theory is distinct from its representation.
I'd say ok, that's a great theory about your model of pressure and your model of temperature in your model of the universe.
And you say, no no, this is a theory about actual pressure and temperature in the actual universe, just like your theory.
In that case your model is not enough. I also need reason to believe that your models of temperature and pressure are relevantly similar to actual temperature and pressure such that relational properties that hold of the entities of your model also hold of the entities they're supposed to represent. If it turns out you modeled temperature as a jpeg representing a picture of a cat, then how is that a theory about the temperature?
Whereas my theory is a theory about temperature simply because my theory says: temperature, that real thing in the world, will do such-and-such.
Your theory assumes these things, but you want to say that the model is invalid because it also assumes these things.
But the more important misconception you appear to have is that you are not considering the human element; no representation of the theory has meaning unless a human interprets it. Programs manipulate symbols; but it is the human who chooses what the symbols mean, and that includes incorporating theories / models implied or assumed about those meanings. It's no different for a theory written down in a book.
Similarly, programs manipulate symbols. It's up to the person who runs the program to imbue those symbols with meaning.
F=ma; that's some coloured pixels on your screen. It's also an expression of one of the laws of Newtonian mechanics. It can be used to calculate the approximate acceleration of a mass after a particular force has been applied to it. But the coloured pixels on your screen isn't doing that; you need to apply your mind.
Similarly, here's a function:
function calc_a(m, F) { return F / m; }