The NOL-DC-CHI-EMY trip I am taking is more than 3 Zones. To my way of thinking, it is beginning in Zone 2(Central) traveling into Zone 1(EAstern), then traveling back into Zone 2(Central, and then on thru Zone3(Western). Of course AGR 2.0 does not have zones anymore.
I agree that it is what it is and further discussion will not change anything. My happy news is that during 2016 I earned Select Plus so will be earning more bonus points through Feb 28, 2018. Probably never reach that level again since all my Amtrak travel is personal mostly LD in sleeper since I live in un-served Nashville, TN.