Yes and to be clear, one uses "TFA" to imply annoyance that TFA hasn't been read.

e.g. "TFA covers this already."

That’s not something I wanted to imply. It can also stand for "the fine article". Is there a better shorthand for "the article linked at top of the page" / "the original article"?

Nope, you just say "the article". But also... nobody's truly offended by "TFA" AFAIK.