Juan,
I beg to disagree with you on a number of points.
First, I completely disagree with your claim that simply because c is a constant, Dx/Dt must trivially go to dx/dt. This is true *mathematically.* My point is that it makes no sense *physically.* I think I made it fairly clear *why* this makes no sense in my essay.
Now, before addressing your next points, let me first address your comments concerning quantum mechanics and quantum field theory. You are taking the difference between the two as being a contradiction. But two things can be different and not contradict. More to the point, quantum mechanics treats time as absolute (i.e. it ignores time) much as Newtonian mechanics (NM) does and thus both are generally interested in obtaining information about positions as functions of time. In the corresponding relativistic extensions of both QM and NM, space and time are now considered together and thus we are interested in functions of position and time (together). This does not, however, mean they contradict each other. In fact, as an example, it is a rather simple affair to derive NM from GR (see for example Shutz or Misner, Thorne, & Wheeler). They can't contradict if one can be derived from the other. The uncertainty relations still hold in QFT (in fact they are sometimes invoked in order to "explain" the spontaneous pair creation).
Now, regarding the points you made regarding discreteness (atomism, or whatever), let me start by quoting from Griffiths: "In principle, the force of impact between a bat and a baseball is nothing but the combined interaction of the quarks and leptons in one with the quarks and leptons in the other." So, ultimately, our classical interactions like that between a baseball and a bat, are really the sum of a bunch of quantum interactions. As you yourself just said, "there exist limits where that discreteness is indistinguishable from a continuum." Precisely my point! That limit is the macroscopic realm of classical physics! Classical physics works because we don't look closely enough or don't care for an increase in precision! But as soon as we do, we run into discreteness. Imagine you're an engineer making a speedometer for a car. Your boss asks you to make this speedometer more precise - say to 2 decimal places. Then he/she comes back and asks you to make it accurate to 4 decimal places. Then he/she wants 6 decimal places, etc. Eventually, though you're measuring a classical value, you're going to run into a *physical* - perhaps engineering is a better term - problem of *how* to get that information from the universe! The most accurate machines are discrete! In fact, the most accurate physical theory ever developed, i.e. in which theory comes closest to experiment, is QED *which is ultimately a discrete theory!*
As for the atomic chemists, I disagree, but then I note that the difference between your view and mine is simply a matter of interpretation. I have done a lot of work on the history of science and have reached a different conclusion. But then again, I know a lot of people who disagree with Thomas Kuhn's take on the history of science (including myself) and yet others who staunchly defend him. It's hard to be "right" when talking about the history of science in such a way.