I would have treated it as singular and used the word “is” rather than “are.”
Nevertheless, I can see some plausibility in considering the phrase “baseball’s marquee franchise” as interchangeable with “the Yankees” and thus being considered plural. This is parallel to, or possibly exactly equal to, the British convention of saying “the team are…” or “the government are…” based on viewing the team and the government as multiple individuals rather than one entity.
I’d be interested in seeing whether the writer of this article treats such situations in this manner consistently. If he does, I would say it’s a matter of style and figure he chose the British norm over the American.
I suspect, as Gary says, that it’s an extension of the practice of treating ostensibly singular nouns that refer to groups of people as plural, something that varies among dialects. But I’m a native British English speaker, and although this is common in my dialect for some nouns, I find this jarring - if I were proofreading I would correct to “is” without hesitation. So it may just be an error. One could test that by paraphrasing the sentence into a more concise form and asking the writer (or editor) if it really feels correct in their dialect to say (for example) the franchise are playing well.
But there’s really no logical objective standard by which you can say it’s acceptable to treat some nouns like this as plural and not others.
My first reaction is that there is no dialect of English (or any other language that I’m aware of) in which adding a qualifier like this affects subject-verb agreement. In principle, either “the franchise are” is okay in a dialect or it’s not.
However, since it’s probably a marginal case whether treating* franchise* as plural is okay or not, maybe you’re correct that when a qualifier draws attention to the “grammatical analogy” it does make it okay. Without analysis, it certainly makes it subjectively less jarring to my ear.