Hi @vp1981, I intend to work on packaging ROOT for some Linux distributions in the next year, and on making it easier for others to package it in other distros too. The idea is to provide scripts for configuring and compiling ROOT and to make ROOT follow FHS more closely, as you propose above. As for the question you have, let me answer it in parts.
About Python
I saw in your configuration that you have python=OFF and python3=ON, please invert that to python=ON and python3=OFF, regardless of what version of python you are trying to use. If you need to compile ROOT against a specific Python interpreter, please set -DPYTHON_EXECUTABLE=/full/path/to/python with CMake. That should solve the problem that you have. There is a minor bug with the python3 option in CMake, so it only works if you are compiling against Python 3.5.