Yes, it does cover that. I copied the part that does, twice. Here it is again.
The amount of initial D is not required or assumed to be zero. The greater the initial D-to-Di ratio, the further the initial horizontal line sits above the X-axis. But the computed age is not affected.
If one of the samples happened to contain no
P (it would plot where the isochron line intercepts the Y-axis), then its quantity of
D wouldn't change over time -- because it would have no parent atoms to produce daughter atoms. Whether there's a data point on the Y-axis or not, the Y-intercept of the line doesn't change as the slope of the isochron line does (as shown in
Figure 5). Therefore, the Y-intercept of the isochron line gives the initial global ratio of
D to
Di.
For each sample, it would be possible to measure the amount of the Di, and (using the ratio identified by the Y-intercept of the isochron plot) calculate the amount of D that was present when the sample formed. That quantity of D could be subtracted out of each sample, and it would then be possible to derive a simple age (by the equation introduced in the first section of this document) for each sample. Each such age would match the result given by the isochron.
It very much gives the impression that you think any scientist who doesn't share your belief that God manipulated parent/daughter elements and/or decay rates must be an atheist. But if that's not what you think, I'm glad.