In particular, if you have a male ancestor at the Identical Ancestor Point but the lineage from them to you passes through a woman at any point in the family tree, you would not get that male ancestor's Y-chromosome via that line of descent.
Or put yet another way, if you are male, you have 2^N (possibly overlapping) ancestors N generations back, but only _1_ ancestor N generations back that contributed your Y-chromosome. Comparing to a different male, the chance that you share Y-chromosomes is naively something like 1/P where P is the size of the male population at the time, while the chance that you share your ancestor sets is a much more complicated calculation, and the article claims it's ~1.
In the first the path goes through both fathers and mothers. This is easier to achieve, and so you get to it more recently. The second is harder and so happened longer ago.
I guess it's kind of like the difference between a permutation and a combination.