Marin County is one of the wealthiest in the US, and in the bay area. Where the wealthy VC guys live, and the heads of the startups that made it.also a small, not so populous County, so percentages aren't as meaningful.
Alpine County has 1167 people total. Not hard to get a high percentage.
There are plenty of counties with smaller populations, and none of them even hit the 2.5% mark, let alone the >=7.5% that Alpine is showing. As far as Marin county, I wasn't surprised that it shows up on the list, just that it was in the highest category. Also, I wouldn't call a quarter of a million people 'not so populous'. Like I said, if you'd have been asked this question before, you'd never have guessed these 2.
I knew CA would for sure be #2 in Jewish population, but I was definitely surprised to see the SF area be such a big part of that. One table I just saw had LA area at less than double SF area.
Bottom line is that barring mistakes in their underlying data, or in converting the data into a map, all the 'anomalies' are going to be explained by relative population size. Doesn't make some of it any less surprising.