This is a classic "YMMV" issue - I have used my WN frequent flyer card at SEA, because that is one of the elite cards that will get you through the elite security queue, when using Horizon, for example, and my AA EP/EXP card at a couple of other airports where I was using WN or DL. But it's not predictable, and depends on the vagaries of the local airport (e.g. SMF has no elite queues at all, though they say they will initiate one "soon").