I looked this Act up, appears it only applies to those coming to the country on foreign nautical/sea faring vessels (perhaps was updated at some point to include other modes of transport) although it's scope is "communicable and transmissible diseases" from "infected foreign ports."
By executive order for "certain diseases" is a bit vague but would imagine they would still have to fit the description of "communicable and transmissible diseases" and hold up to scrutiny under the courts.
Sure I get your point between the lines, they can try to warp these laws with executive orders to fit whatever delusional narrative RFK, Jr is pushing but this is also why it's important to call it out, push back on it, and demand accountability.
Perhaps getting ahead of the problem presently , which is the violation of privacy and patient rights (as well as safety) by them discussing the idea to create a registry of people with certain diagnoses.
RFK, Jr had he had this role during the pandemic probably would have pushed to ban vaccine requirements rather than enforce better containment of COVID in the early pandemic days but the guy has an unhealthy paranoid fixation with claiming imaginary links between vaccines and autism instead 😒