Ever notice how you never hear humans playing music that humans aren't capable of learning to play? I think there may be some selection effects at play here...

There are probably no more than 100 people alive that can make their way through Bach's 2nd Partita for violin.

I'm pretty sure you're underestimating that by...a lot. Fermi estimate time:

Bach's sonatas and partitas for solo violin are a cornerstone of the violin repertory. We may therefore assume that every professor of violin at a major university or conservatory has performed at least one of them at least once, just like we may assume that every professor of mathematics has studied the Lebesgue dominated convergence theorem. How many professors of violin are there? Let's just consider one country, the United States. Each state in the U.S. has at least two major public universities (typically "University of X" and "X State University", where X is the state); some have many more, and this doesn't even count private universities. Personal experience suggests that the average big state university has about one professor of violin. There are 50 states in the U.S., so that's 100 people already right there. And we have yet to count:

• every other country in the world (including European countries like Germany where the enthusiasm for art music in general and J.S. Bach in particular is likely to be much higher);
• private universities and conservatories in the U.S.;
• members of the violin sections of professional symphony orchestras throughout the world (again, on average one in each U.S. state);
• professional concert soloists (there may be more of these than you realize)
• the students of the aforementioned professors (between 5 and 20 in a given semester, at least one of whom will typically be playing one of the sonatas or partitas that semester).

Thus, it wouldn't surprise me at all if there were at least 10,000 people alive who have performed one of the sonatas and partitas (to say nothing of those who would be capable of performing them). There are six of these works in total, so we can divide this already-conservative estimate by six to (under)estimate the number who have performed the Second Partita in particular. (This is likely an underestimate because many of them will have performed more than one -- indeed, all six, in a fair number of cases.)

A glance at the recordings available on Amazon, sorted by release date may help put things into perspective.

The estimate "no more than 100 alive who can make it through" would be much more appropriate for a difficult contemporary work (like, say, Melismata by Milton Babbitt) than a 300-year-old standard.

It might be more accurate to say that pretty much everything, including what we call biology and physics -- humans are the ones codifying it -- is memetically selected to be learnable by humans. Not that it all develops towards being easier to learn.