In reviewing more of the beer brewing literature, I found an interesting observation in Handbook of brewing By F. G. Priest, Graham G. Stewart in the discussion of microbiology about the decline of serial repitching in brewery operations. It has little to do with genetic drift (though perhaps for some strains that is a problem). With serial repitching of yeast, it also brings along some unique (to that brewery) bacteria. These bacteria are not really harmful to the beer, but they may add some unique minor flavors that weren't considered flaws, but simply part of the house style. The authors also mention that the desire (they use the term need, is there a regulatory requirement?) in the brewing industry to reduce N-nitrosamine concentrations has led to less serial repitching.
Now I know some of you may be thinking at this point "Enough with all this science! what does this have to do with bourbon/whiskey!?!" Many on this forum are very interested in how the old pre-Prohibition whiskey differed from it's modern expression. Some even would say it was better, in the sense perhaps that it had a more robust flavor profile, perhaps greater complexity, if only slightly.
I'd suggest that the decline of serial repitching is one of the many differences between modern practice and 19th century practice. And the only way to know what the actual differences really are is to go make some whiskey and taste it.