I think this is one of those things where the meaning has evolved over time, at least as someone who's been on Slashdot since the early '00s but only joined HN a few months ago. Originally, you'd only see "TFA" as part of RTFA, generally with the assumption that the person you're replying to had not read the article. ("If you'd RTFA, ..."; "Maybe you should RTFA.")
But "TFA", although it derives from "RTFA", never seem to had the same negative connotations. It's just that sometimes you want to refer to the original article in question, but "original article" is long to type and/or ambigious. (Do you mean the news article from the NYT, or the scientific paper the NYT article is reporting on?) And "TA" is too short for people to clearly know what you're talking about (And did you mean "teaching assistant"?) "TFA" is short and unambigious: it always means the article linked to from the main page.
Long story short: Although etymology would suggest that "TFA mentions this" is as aggressive as "Maybe you should RTFA", in actual developed usage, they're very much not the same.