Amtrak is pricing at market rates, because the product it is offering in the NEC is generally a valuable product. Likewise, its rates elsewhere are much lower, because that's what the market will bear in those markets (the Amtrak product is less valuable).

I've always thought Amtrak should offer a limited number of restricted tickets at lower NEC rates to provide some fairness.

If Amtrak charged less, it would just be giving money away in the absence of huge additional capacity. If global warming were a real concern rather than a concern du jour, then perhaps we would fund and provide that capacity.