Update math/eigen3 to latest upstream release

Release notes are at
https://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.9
One of our patches was for issue 2011, which is resolved upstream,
so that can go. The other patch is not needed anymore either.

While here, drop the gl (USE=gl) dependency. This turned out to be
needed for tests that aren't built anyway. I mini-exp-ran this by
test-compiling all the things that showed fallout in the previous
Eigen update.

Referenced PR is about gl, not about updating Eigen.

PR: 251939