I guess there are different agents at JFK...I've used Flagship Check around a dozen times in the last six months and would say maybe half the time I've had an agent take me from check-in to security (I've always accessed as a OW Emerald rather than being in intl/transcon F). The TSA people don't seem to be too bothered whether an AAgent is there or not...although usually I'll find when the AAgent is there they'll do a quick glance and mark the boarding pass rather than the two or three "ident checks" they often do when I'm there by myself (I'm old school and use the non-electronic BPs).