Yes, lowering it will alter all of the alignment angles, particularly toe and camber. The tie rods actually need to be shorter to compensate for the new positioning of the spindle to the steering gear. You will also find that the wheels are cambered out at the top as well.
I would get the toe close so it doesn't scrub too bad, then gat it aligned, as camber needs to be reset first to get an accurate toe setting.
