Not sure about previous versions, latest versions should merge them on reading.
...I think I tested that out before, but I can test again just in case.
OTOH, current engine actually supports multiple config files, read-only one in game installation folder (as default, and for backwards compatibility), and writeable in user "saved games" folder (this currently is Windows setup, other ports may have only one file in practice). Their contents get merged without problem, second config values overriding previous one, but not erasing options that do not exist in second.