That's a misunderstanding of what the data actually represents. It's (almost but not quite) like saying almost everyone in the UK is descended from Richard III, simply because after so many generations, most people in the UK do have some of his DNA.
It's also true, though probably politically uncorrect to say it these days, that a viable breeding population requires fewer males than females, a ratio of 100:1 or more would be feasible. Mitochondrial DNA analysis would probably give a more useful picture of the actual size of the breeding population at the time of those "super-grandfathers".
On the other hand. It would seem to indicate, that the concept of a massive flood event, wiping out huge chunks or even all of the Earths population, a very long time ago (e.g. 5,000 years ago). Could have reduced the population to a very small number of initial survivors, perhaps 3 men and a few or so women. Then many thousands of years later (i.e. now), there could be hundreds of millions or billions of people from that original event.
The points you made previously about diversity of the over all (worlds) population, and scattering of it, to many parts of the globe, are very good ones. So my explanation above, might need a number of changes, such as to the exact time of the flooding event(s), and other things. To account for how we are, where we are (as regards the worlds human population).
N.B. I'm NOT trying to agree (or disagree) with the flood (Noah) theory, just trying to be somewhat scientific.
Also, I'd prefer to still take into account the nuclear DNA (nDNA) as well, as the more information that can be used, the more likely, accurate predictions of what really happened, can take place.
Anyway, the ratios of taking just 2 animals of each type, wouldn't really work out, as I see it. Because, if a particular animal, needs to eat thousands (each year) of much smaller animals (or fish) to survive. Then just having a single pair of its food source, wouldn't keep it fed.
Also, I'm not sure that the entire Earth could be fully, 100% flooded (land wise), for a period of time, then a huge amount of that water, disappears. Really works out, as floods usually just affect, a relatively small percentage of Earth, at any given time.
I suppose the flood, could just be in the area, that the then, human population, was living, a very long time ago. Before they became more adventurous, and moved around the globe.
The problem with stories, is that it is very easy to just twist them, to fit the available facts. So, you can't really tell, if they are true or not.