No, the magnetic pickups will only make a difference when using the guitar in mag pickup mode.  All of the modeling is done through the piezo pickups in the bridge.  The mags have no effect on the modeling at all

I would imagine that Line 6 released the 69s because some folks prefer the 3 single coil strat-type configuration for both more classic esthetics and sound.  Some of us (like me) prefer the HSS "fat strat" config.  Now Line 6 can offer both