I do not get any error during the "make third_party" or "make cc".
I have ensured no protobuf 2.6.1 headers are used during above commands and both commands work well, no errors are encountered during installation of or-tools.
As per my analysis, I am using Qt framework and Qt libraries are using gtk libraries. These gtk libraries use mirprotobuf library that is compiled using 2.6.1 version.
Ubuntu 16.04 has protobuf 2.6.1 library by default and gtk and other system libraries depend on it as they are compiled using 2.6.1 version. When I removed 2.6.1 protolib libraries Ubuntu Desktop did not start after reboot.
Since I can't compile gtk and Qt libraries with 3.6.1, I am retrying with Ubuntu 18.04. I hope I will not encounter this issue as I have read somewhere Ubuntu 18.04 has protobuf 3.6.1 as default library.