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As you can infer from the name, pybin11_catkin is a:

Catkin wrapper for pybind11

which basically means:

This repository wraps the recent releases of pybind11 for use in catkin-based projects.

Among other things, this makes it easy/ier to build / use pybind11 in Catkin (and Colcon) workspaces, and consequently, ROS packages.

Other advantages would be the use of this package across different OS (which may not have pybind11, but do support Catkin workspaces/ROS) and a more homogeneous development environment (pybind11 available at the same version everywhere).

See ipab-slmc/pybind11_catkin#3 for what appears to be a discussion around utility of the package. This links to arturmiller/pybind11_examples for some examples.

I would rather use the one from Ubuntu

By all means do.

If you are on an OS which packages pybind11 at a suitable version and you don't need/want to depend on the Catkin wrapped version, then don't use it.