I am currently thinking of integrating the KissFFT functionality into a commercial closed-source project.

This resource http://eigen.tuxfamily.org/index.php?title=EigenFFT states that KissFFT is under a GPL/LGPL license.
However, the official kissFFT project page on sourceforge defines the license to be BSD, which is more permissive: http://sourceforge.net/projects/kissfft/

Which is declaration is the correct one when using KissFFT in Eigen?

This page is rather out to date. The FFT module within Eigen in MPL2 just like the rest of Eigen.

And to which FFT implementation does the MPL2 apply?
KissFFT = MPL2
FFTW = GPL

is this correct?

correct.