Can't you just use model.cfg animations for this?

I don't think, because you're talking about the fact that we can do an animation with this ticket? If that's the case, we always stay limited, some vertices need to be in specific places calculated on the moment T, and the fact of creating animations prevents you from having precise things because it's pre-defined. (Correct me if I'm wrong, and you weren't thinking about that)

And, we could use bones; but I think that additional data on an object that must be "simple" (depending on the context of use) seems greedy to me, unlike changing the position of a vertex.

You can assign a single vertex a selection name and animate it for all axis. Instead of setting the position via script, you would translate the target position to a local animation value for the axis. You would need to name all the vertices you want to move anyway in order to know which is which in script. So the step from doing that to just giving it animations is quite small.