I'm pretty sure the stacked jetway is due to the fact that departures are on the top floor but international arrivals need to be delivered to the lower level. It's just when you arrive on a non-international plane you have to go uphill to stay in the sterile area and then if JFK is your final destination you walk to the middle of T4 and go down an escalator to get back to the arrivals hall and baggage claim (but past customs and immigration).
In normal times all of the gates with that setup are used primarily for international arrivals and departures (or JFKLAX) and then once those planes arrive/depart, they are used as overflow for other flights.