Yeah I have to admit that this puzzled me as well. I think Kevin and the rest of the YC folks have every right to do whatever they please with this process, and am not bothered in the least by the fact that Pinboard wasn't chosen, but reading Kevin's explanation somehow made me think that some of those WOULD be reasons to select it.
Pinboard is in a relatively unique situation amongst all the other companies in that it is beyond finding product-market fit -- it's got an established userbase and a founder with proven chops and a large following. It seems like he is in the exact position where something like YCF can help pour gasoline on the things that he's doing that are already working.
I understand YC's tremendous focus on finding a right fit with founders when they join the regular batches. But, at least at first, it's not entirely clear that this criterion should hold as much weight with YCF. They'll talk less frequently, invest less money, etc. -- maybe the optimal strategy for YCF is in fact focusing much more on the present stage of the company and whether or not the little bit of cash/partner influence can cause an inflection??? Who knows, really... but it sure sounded like accepting Pinboard -- not in spite but because there were these issues with Maciej -- would make it an especially interesting case to try out.
If the point was to experiment I think YC missed out on a big opportunity.