I’m not a prophetess 
but I think it very likely that small things like this will continue to stack up and evolution via common ancestry may start to “stink.”
[/quote]
“Stink”? You are misinterpreting that paper and ignoring the data for the explanations that account for the disparities between the human and chimp Y-Chr.
Let’s try this again because I know at times you get these things but need sometime to figure it out. There are two talking points here according to the section you quoted, “percentage of shared gene families” and “overall Y-Chr architecture”.
First, the phylogeny of the great apes (including us) derived from the Y-Chr agrees with the phylogeny derived from their autosomes, further confirming our shared ancestry
Second, despite our closer evolutionary relationship to chimps based on the Y-Chr phylogeny, the percentage of gene families we share with them are less, but more with gorillas. Why? The answer is a higher rate of gene loss in the Pan lineages (chimps and bonobos) relative to humans and gorillas. According to the paper, the common ancestor of us, chimps and gorillas had 25 gene families and you can see it in this tree diagram (from the paper, Fig 2):
That common ancestor is the root of the tree and you can clearly see the 25 gene families it had. Evolution starts and gets to us, but a lot of changes had happened to that collection of ancestral gene families in the different lineages. Out of the 25 ancestral gene families, chimps lost 8, bonobos lost 7, while we and gorillas lost 1. From the figure, the common ancestor of chimps, bonobos, humans, gorillas and orangutans lost one ancestral gene family, while the common ancestor of only chimps and bonobos lost 6 gene families, giving a total of seven ancestral gene family deaths: after splitting from their common ancestor with bonobos, chimps went on to lose one more ancestral gene family, raising its gene family loss to eight. This beautifully explains why the percentage of gene families shared between chimps and humans relative to that shared between humans and gorillas is lesser, despite our closer relationship to chimps.
Third, the overall architecture of the chimp Y-Chr differs from that of humans despite their recent shared ancestry. Is this surprising? No, as per the data in the paper. For instance, chimp Y-Chr is half the size of human Y-Chr, but this is expected considering the significant number of gene loss events (some of which are deletions and gene deletions shrink genome sizes), for example. In general the evolutionary rates of Y-Chr’s (be it in humans, chimps or other great apes) is higher relative to the autosomes and X-Chr’s, explaining why they are much smaller size relative to the aforementioned chromosomes. Since this rate is much higher in the chimp Y-Chr, its not surprising that is smaller in size than that of humans.
Then you have a strawman perception of scientists.
What’s more amazing is your ignorance of the data right in front of you from the paper you cited.
You are right that it is pointless arguing about it because the data is right there in front of you and it settles the challenges but you choose to ignore it.
Looking forward to that, but I hope you take your time to understand the data and come to a conclusion supported by that data.