IMO the breakfast pricing is still reasonable considering it's on a train. Our local Denny's charges $12.29 for a veggie omelet with potatoes and toast, plus $3.69 for orange juice or $3.49 for a coffee and $3.99 for four sausage links. Assuming the breakfast comes with a side, an equivalent Denny's meal would be $17.97 + tax (I'm using $1.99 instead of $3.99 for the sausage links since Amtrak only offers 2 on the side.) Amtrak pricing generally includes any relevant taxes, so the difference between getting the meal at Denny's here versus on board Amtrak is less than a dollar.
Lunch seems high as well, but if it's coming with dessert and a non-alcoholic beverage I'm not outraged over the price. Again assuming around $12 for a comparable Denny's burger (the closest is $12.29 for a double cheeseburger with fries, but they won't let me price a single cheeseburger and I don't know how the patty sizes compare,) fries vs. chips being roughly equal, plus a $3.49 drink and $4.99 dessert, and a comparable Denny's burger is $20.48 + tax. Again, tax would add probably another dollar to dollar and a half here, so it's roughly $3 more on board versus at a chain restaurant of similar quality.
If anything, dinner is the one that's relatively unaffordable, especially if you don't drink alcohol. There's no flat-iron steak at Denny's, but a sirloin with the fixings is $14.49, and a T-bone is $17.69 with the fixings. Add the same $3.49 drink, $4.49 salad, and $4.99 dessert and Denny's pricing is between $27.46 and $30.66 - so there's easily a $10 upcharge and possibly closer to $15 if a sirloin would be more comparable than a T-bone. Once you add the complimentary alcoholic beverage it becomes in a similar ballpark, or if you do a different starter the value may be different, but I still think Amtrak's highest-price-differential meal is dinner, and breakfast and lunch are still the more reasonable meals to pay for.