Are OS X systems with manually set, complex (128 character), root passwords more, or less, secure than the vanilla system freshly installed?
Enabling the root user decreases security.
Apple turns it off by default which means that someone trying to perform a remote log in both has to guess an admin user name and the password. It's not a huge decrease in security, since all admin users can become root knowing an admin password, but by enabling root, you have either doubled the exposure (the first account on a Mac has to be an Admin account and the root doubles the exposure) or if you have several Admin accounts, it increases the number by one.
Since it only takes one password to be guessed or "stolen" - having fewer openings is a more secure stance from a numbers and chance standpoint.