At the moment, there are still some hard paths in the build system, so it’s difficult to make ROOT work if you set configuration directories individually, like you are doing in your build script. I recommend that for the time being, you install ROOT into /opt/root and add /opt/root/bin to $PATH and /opt/root/lib to $PYTHONPATH. Please make sure to configure ROOT with -Drpath=ON and -Dsoversion=ON, and use the same compiler that is used for the rest of the system to avoid ABI incompatibilities.
In the future, we will try to make the installed files go automatically into the right places according to their purpose instead of many of them going to /etc/ as happens now. Please let us know if you have any other questions. It will be nice if we can make ROOT available to at least the major distributions in the next coming months.