There's also points from the CC and/or status (and/or seasonal/special offers). That $1000 ticket might get you 2000 points. With the CC that becomes 4000 points, at Select Plus with the CC 5000, at Select Executive with the CC 6000...and Double Days can add another 2000 on top of that.
On the other end of things, Amtrak points will tend to get you somewhere between $0.02 and $0.05, depending on how they're used (and I've heard of people getting even more out of them...something like Denver-Miami in a roomette can easily run over $1200 but only costs 20,000 points)...so sometimes a point buy makes a lot of sense if there's a bonus deal going on at the high end, while at the low end...not so much.