OP is right. If you apply SCEA to Yale, you may still apply "priority" (Nov 1st deadline) or EA to your instate (flagship) school. They clarified this when we visited. Also we called Yale Admissions again to clarify when my D was applying SCEA to Yale and also considering U-Mich. They said no way for U-Mich and Yale EA (must chose only one) as we're not from Michigan.
D got admitted to both Yale - SCEA and our state flagship school - EA. This clear example - guided by specific answers (by Yale) to specific questions from us should settle this, I think.