I've now read the two papers, the original 5 sexes one and the 'revisited' one from 2000. The first one is about intersex people, and argues against intersex people having their genitalia 'corrected' early in their life to fit a more 'normal' appearance of male or female. She doesn't mention transgenderism at all in this paper. At the end of the paper (in my link, which looks like a scan of the paper original) there is some correspondence, which includes a letter from John Money and also one from Cheryl Chase, who Fausto-Sterling talks about in the second paper. There is also a reply to some of these comments from Fausto-Sterling, where she says that she was being 'ironic' (see screenshot).
Her classification of intersex people as 3 separate sexes distinct from male and female seems unsympathetic and offensive to intersex people. If this is what she was suggesting was 'ironic' in her tweets, I assume it's trying to minimise the offence she had caused.
The second paper is the one in which she starts to conflate intersex and transgenderism, using the idea that because some people are not clearly and unambiguously male or female, therefore people who are unambiguously male or female might have an opposite sex gender identity which makes them not either male or female, similar to the way in which she thinks someone with an intersex condition is neither male nor female.
It might seem natural to regard intersexuals and transgendered people as living midway between the poles of male and female. But male and female, masculine and feminine, cannot be parsed assome kind ofcontinuum. Rather, sex and gender are best conceptualized as points in a multidimensional space. For some time, experts on gender development have distinguished between sex at the genetic level and at the cellular level (sex-specific gene expression, X and Y chromosomes); at the hormonal level (in the fetus, during childhood and after puberty); and at the anatomical level (genitals and secondary sexual characteristics). Gender identity presumably emerges from all of those corporeal aspects via some poorly understood interaction with environment and experience. What has become increasingly clear is that one can find levels of masculinity and femininity in almost every possible permutation. A chromosomal, hormonal and genital male (or female) may emerge with a female (or male) gender identity. Or a chromosomal female with male fetal hormones and masculinized genitalia - but with female pubertal hormones - may develop a female gender identity.
I'm not convinced that anything she is saying now indicates that she is retracting this view.