This is a package that stores the eigen header files. You can either use it directly, or better still, interface it through ecl_linear_algebra which provides a few extra features.
It installs into include/eigen3.1.2/Eigen, firstly so that it keeps the installations separate should we happen to install multiple eigens into the install space, and secondly, it puts it in the root rather than nested inside ecl to keep it visible.
Users should only use the internal eigen if they will only access eigen from ecl for every part of the code in their eventual binaries. We do this often for embedded installs where the dependency list is slim, but eigen does happen to be one of those, but lacks an installable deb or similar.
Mixing eigen's can have compatibility issues. For example, utilising eigen 3.1.2 from ecl would not mix with a pcl that uses a system eigen 3.0.0.