Looking at the simplified diagram of an alternator, the flux "linked" with the conductor is maximum at 90, 270 degrees, is also when induced EMF is maximum. So isn't the main flux in phase with the induced EMF, or are my assumptions flawed?
It's important to note that in an alternator, motional EMF is created which depends on the spatial angular displacement between an uniform magnetic field and a conductor perpendicularly placed. A time varying EMF is induced only because the angular displacement is a function of time, not the magnitude of the magnetic field itself.