How to design a city?

True, but as I'm sure you're aware traffic modelling also bears a few hazards, as often the models are heavily simplified and streamlined to enable engineers to show that schemes fulfil something like an 85th percentile capacity peak hour requirement, as part of whatever scheme justification they have to do.

They are also only as good as what is put in, i.e. if no motor traffic reduction or a projected increase is factored in to start with they will do a huge disservice, as they often lead to business as usual and often to increased motor traffic capacity. We are still very far from sophisticated models being applied generally. It is also quite hard, perhaps impossible, to model cyclists and pedestrians.

Unfortunately you have clearly been given modeling data in a incorrect light. The point of models frequently is not in general to get out a number. It's to ascertain what are the general mechanisms behind a physical problem are, what the relationship is between factor and how strongly they are linked. It should also be fully stated in what regions / conditions the model is valid. As far as traffic modeling goes you would have to have several models for different situations, much like every other physical situations.

I expect most government models are using very old methods, but employing some decent mathematicians / engineers to do the job is prob not high on the department for transports list. Many government departments just have some program that they bought and no qualified people to a actually model.

As far as modeling cyclists and pedestrians into a traffic flow I see little point how do you mean? If you mean their individual flow and how street planning allows the flow of ped / bikes, in which case that should be easy. Or do you mean adding ped / bike flow in with vehicular flow? If so there is little point as the same effect can be achieved in other ways which I ma willing ot discuss at a pub with pen and paper.