It sounds like the model is more postdictive than predictive. Not useless, but more like measuring a huge number of right triangles to determine the ratio of side lengths, versus deriving the pythagorean theorem.
There is perspective and there is selling a work short. This is much more than a blind statistical model of the parameters. In fact, your criticism would apply just as well if not more to the Higgs search methodology.
They develop a number of submodules that each use an appropriate algorithm or branch of mathematics to best represent the interaction. To integrate them, results from the previous time-step feed each model as appropriate. The derivation of the correct mathematics and algorithm to use and the best way to connect them is anything but measuring a bunch of sticks.
Plus they were able to do some predictive modelling and pointed a direction for a novel result. From the abstract: "experimental analysis directed by model predictions identified previously undetected kinetic parameters and biological functions." This is not about simulating organisms, it is for accelerating experimental discovery of interactions, dynamics, parameters etc. This is a proof of concept that a technique which may one day contribute to saving lives is viable.
