The effect of a lower price (discount) will be fewer points earned - points are earned 2 points per dollar spent on a ticket. Pretty much the same as before. Also, you are aware that such discounts apply only to the base (coach) rail fare - The "accommodation" charge (extra for sleeper, business class) is not discounted.
For redeeming points, it is based on the non-discounted fare which means it will cost more points! If you go through the process online, select senior, or some other discount, there is a "fare alert" which if you were to read it, informs you that the redemption is based on the non-discounted fare.