That's the actual answer, 1, but what the author was claiming is certainly possible too. Just because a meme can be used in just about any way, some are used in some ways a lot more than others.
I think the mistake in the Daily Beast article is that the author's source were users on Twitter who were as close to being anonymous as possible. The same author acknowledged that memes are often ironic and used for whatever, but when you have to present an angle, I think they did so with some sources that are as good as you're going to get for memes.
Also, that author couldn't just come here and read the Pepe article. We all know our articles may be slow to be updated. And, as you say, any update may have just simply been omitted, because we accept the reality that memes can be used for whatever reason.
That's not the understanding of someone not involved in Web culture. I don't think they had time to come to incorporate culturally shared understandings of a community they aren't a part of for the sake of an article they were assigned to write but probably don't care about…
Because, let's be real: we're dorky nerds. We insult other people for not knowing about stuff they don't even care about.
This is about as good as you're going to get for an a Journalism BA not born in the 1990's or later.