The opinion piece was from an MD who was all set to criticize RFK until she actually looked at the literature.
1. I can't speak to the criticism other than saying there's always going to be messy data in a field study. The authors did address the boy-girl discrepancy in the abstract and their conclusion was a little different. "A 1-mg/L increase in MUFSG was associated with a 4.49-point lower IQ score (95% CI, −8.38 to −0.60) in boys, but there was no statistically significant association with IQ scores in girls (B = 2.40; 95% CI, −2.53 to 7.33). A 1-mg higher daily intake of fluoride among pregnant women was associated with a 3.66 lower IQ score (95% CI, −7.16 to −0.14) in boys and girls.". Basically they are saying for relatively normal fluoride consumption in pregnant women there's no effect on girls but a fairly significant effect on boys. If you double the fluoride consumption in pregnant women, there is a negative effect on boys and girls. Even if it is just boys, that seems like an issue we need to address.
2. And yes, the American dental association did confirm the benefit to fluoride. No one is saying there aren't benefits. The question becomes do the benefits outweigh the costs and there's some pretty good evidence they don't. We also need to recognize that there are other ways to get fluoride such as toothpaste that don't have those same negative effects.