I think the matplotlib 3.9.2 cp313t wheels (or at least the manylinux x86_64 one) were built using the problematic pybind11 2.13.1. If I create a new 3.13.0t virtual environment using pyenv and install the latest contourpy (1.3.0) and matplotlib (3.9.2) wheels and run some code that uses both matplotlib and contourpy:

$ PYTHON_GIL=0 python
Python 3.13.0 experimental free-threading build (main, Oct 26 2024, 16:31:15) [GCC 13.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib.pyplot as plt
>>> plt.contour([[1,2],[3,4]], levels=5)
Floating point exception (core dumped)

If I then install the latest matplotlib nightly wheel (3.10.0.dev900+g835d5125a3) which definitely uses a later pybind11 the above code works fine and I can plt.show() successfully.

But maybe the fact that the matplotlib 3.9.2 cp313t wheels are problematic is moot. We aren't fully claiming free-threaded support until there is a matplotlib release containing PR #28819 and a kiwisolver release with the equivalent (nucleic/kiwi#186). Until then if you try to import matplotlib in a free-threaded venv you get the warning that matplotlib/kiwisolver aren't claiming they can run safely without the GIL and you have to, at your own risk, use PYTHON_GIL=0 or equivalent.

So given that matplotlib 3.10 is imminent and includes #28819 (and hopefully this PR) then I think we are OK to point users towards that release if they want free-threaded support. We can't really do a 3.9.3 release including #28819 as that would also need all of the recent pybind11 PRs which is not appropriate for a patch release.