I've seen secondary screening coming back from Spain to JFK

My guess is the airlines have done their own risk assessment of threats and how good they think the airport screening/security is. They do this additional screening to attempt to lower their risk to an acceptable level to them to continue operations on a route or from a specific country. Threat intel is constantly flowing and threats can change so it wouldnt surprise me to to see it be more dynamic as to where the airlines focus these efforts. There are not only external threats but insider threats to consider as well. I have seen certain airlines conduct security investigations/screening before even giving you a boarding pass (i.e. you cannot print it on your own, it says obtain at airport). So you do the pre-screening, airport screening, and then possibly screening at the gate. Plus don't forget passport control so sometimes the whole process of arriving at the airport and getting to your gate can take a full 2+ hours under normal circumstances.