Neither of those examples have anything to do with if a publisher was given access to the source. Those seem to be more about those games being developed in a time when source control and backups were handled more loosely within the industry as a whole.

And that does not only apply to games, certain parts of MS office do not have source available anymore so MS has done binary patches to fix bugs, pixar almost lost part of a movie but an employee happened to have a offsite copy at their home.