Rusty - I am well aware cars from these sets ran into the 1960's and beyond. However it is hard to justify taking a $300 car and repainting it for later use such as Penn Central or Amtrak. Your pictured examples of the 1:1's are in museums or charter service which was not the case back in the 1960's and 1970's.
An example is your NYC Hickory Creek which I believe went right from NYC ownership to the Ringling Brothers circus then to a museum. So it is useless to me for Penn Central or Amtrak use as I'd like to be reasonably accurate in the use of appropriate models. Now if we are talking about a California Zephyr dome-observation some saw service with Burlington Northern then Amtrak - could make a case for that but at this time Scott is not offering CZ passenger cars. The Santa Fe 'Acoma' (another of your examples) never saw use with Amtrak as it was sold in 1971 to someone from Ohio and later rebuilt for charter work. So you can see I am not a "toy train guy" who is clueless about later service / preservation of equipment in the real world - I do my research! I'm also not a rivet counter who demands 100% accuracy but I like to be plausible and close as possible. If most cars in a set can be used for my era I may consider same but if most didn't I'm less likely to buy.
I'm also aware how Scott has trouble getting reservations for the proposed Amtrak Amfleet I project in O-scale. GGD has also had trouble selling sets decorated for Amtrak in O such as the Santa Fe 'El Capitan' hi-levels - think only three sets were made in the first run. So while it should be 'easy' to offer an Amtrak version of a set most times there is not enough interest to make it economically feasible for the factory to do. If you think Amtrak is not popular I bet Penn Central will blow it away in that regard.
I realize I'm in the minority here when it comes to what I like and am aware compromises have to be made at times in model railroading. If my square peg does not fit the round holes so be it. It is my money and I need to decide if I can live with the historical inaccuracies or possible repainting (which is a shame in itself given how nice GGD offerings are) work if that avenue is pursued.
If you wish to buy all three sets and run them side by side on your layout or mix them up more power to you but that is not my money or style. So if Scott had offered the Budd stainless edition of the NYC Empire State Express I would have pulled the trigger on a set in S as it would be much more useful to me for Penn Central / Amtrak use. I need to do what is best for me as I do not have unlimited funds to throw at this hobby like most of us so need to be careful about my purchases. Hope that you can understand that.