It's not really syndication. The New York Times has partnerships with The Bay Citizen and several other regional news nonprofits to publish articles in their regional editions on Fridays and Sundays. The articles go through The New York Times's editorial process, not a completely separate process like the Associated Press.

In theory, The New York Times won't lend its imprimatur to articles it doesn't deem worthy, so I don't see why the newsroom that the reporter sits in is an issue.