I've been wondering about this, too. I think it's got to do with the fact that he's just collecting data points for that incident field - the Ex(10) is actually a location 10 cells into the simulation space. The T<100 has to do with the propagation of that wave from one side of the simulation space to the other - he wants to stop after 100 iterations of the field calculation, which I think would be about where the signal would hit that dielectric medium if you look at Fig. 1.5.
If somebody has a good explanation of how this works with the Fourier transform, that would be awesome!