If you are booking three tickets, there may be an assumption that you will need to be seated together, and that precludes you being offered the lower fare class. If you book individually at that lower rate, there is no seat selection - you will be not be guaranteed a particular seat and could be seated in separate places on the train. The other option if there are three of you is to book a table (the mesa fare) which is for four people, but appears to be similar in individual cost to just booking three seats. This would also have the advantage of ensuring you are sitting together.