Do they factor in natural evolutionary pressure and change of the virus?
Not at all. Meta population models use some type of stochastic discrete PDEs and agent based models just infection probabilities. This is an over simplification but just so you have an idea. You can get the gritty details in the papers above.
Can you comment on the models that are used for simulating outbreaks? Do they factor in natural evolutionary pressure and change of the virus? In the case of smallpox, you have something fairly stable, but influenza is highly variable over time. I can't imagine how one does that but it would be cool to know if it's possible.