I've not had a Unity mount before, am I correct in thinking both mounts you have result in 2.26" optic centerline, e.g. they'll line up with each other but the magnifier would sit too high for an absolute or lower 1/3 cowitness height mount?
That is correct. When used in conjunction, the mounts will "cowitness" - the magnifier centerline will sit on the exact same centerline as the aimpoint micro if both are using the unity mounts.