Amtrak's reservations system, ARROW, is not the newest system on the block. The Texas Eagle and Sunset Limited's practice of hooking up in San Antonio and selling through seats on the days that the Sunset runs would confuse the heck out of it, so the simplest solution is to create virtual train numbers that represent the number of through seats (i.e. seats from CHI all the way to LAX).

I don't know the exact numbers, but my guess is that 21 is the "virtual" train for the portion that ends in San Antonio and 421 represents the "virtual" train whose cars are attached to the Sunset Limited and continue on to Los Angeles. (That's just a wild guess; Alan or someone probably knows for sure.)

Now, because the computer system thinks that it is two separate trains, it prices them separately. The base fare is identical for both "trains," but
Amtrak sells fares in a strict, linear bucket system, where the more seats are sold, the higher the fare goes. (See my epic post here for info on how the bucket system works.) The answer to your question, then, is that more seats have been sold on "train" 421 than on "train" 21.

In your case, it doesn't matter, because you're getting off before San Antonio. The seats in both "trains" are identical, and you receive the same amenities (access to the Sightseer Lounge car, the lounge cafe, paid meals in the dining car, etc.), regardless of which "train" you book. So, you can, obviously, book the cheaper one!