There was absolutely no guarantee that he would be confirmed. He only made it through to the full Senate hearings by a single vote as far as I recall and that could easily have gone the other way. I think it's most likely that the timing of the FDA announcement was just coincidence that people might be attributing to him on the basis of wishful thinking and the desperation to show that he's done something positive rather than any concrete evidence.
There are things that RFK Jr has said and done that I do very much support. Equally there are some where he's made himself look an absolute idiot when there was no reason to do so, particularly in relation to the field of medicine. We'll see what happens over the next few years. He may have some success reining in "Big Pharma" (and I'd be pleased if he did), though ultimately I think he'll struggle. I suspect his environmental credentials will either have to be jettisoned or will bring him into serious conflict with the Orange Man Baby. "Drill baby, drill" is hardly going to sit well with his previously espoused views on fossil fuels. Perhaps he'll deny that he ever held those views too.
My feeling is that the wheels may come off when his apparent desire to reduce the drug use in meat production, or the levels of pesticides used on fruit and vegetables has to be balanced against the likely consequence of increasing food prices. I can't see that going down well, and Trump has quite a lot of form for suddenly turning on people who are no longer "on message".