That's true of any simulation or model - it's only as good as the data that goes into it.
The exciting thing is that with this model, they can now rapidly iterate between the behavior of the model and the behavior of the real organism, see where the gaps in knowledge are, and work to fill them in.
>That's true of any simulation or model -it's only as good as the data that goes into it. //
Models can be predictive, indeed that's one of the main reasons to create a model to observe behaviour that otherwise might not have been expected.
A theory in physics for example is a model with proven predictive powers, the model [theory] 'knows' some aspects of what can be observed before those things can be confirmed empirically.
But as you indicate new empirical data can shows flaws in a model just as it can in a scientific theory.
The exciting thing is that with this model, they can now rapidly iterate between the behavior of the model and the behavior of the real organism, see where the gaps in knowledge are, and work to fill them in.
(I'm happy to see M. Genitalium getting attention, since I made a Java genome display for it 14 years ago http://www.righto.com/java/genome/MG.html)