I wouldn't necessarily say this is the wrong forum to post your questions on as this forum does get a lot more exposure than the 3RS forum. You ask some great questions. To address the issue of what was prototype for the El Capitan, you are correct that E8s and PAs did not pull that train. Up until 1967 F7s almost exclusively pulled the train when FP45s took over. That doesn't mean you wouldn't necessarily see a random F3B thrown into a consist every now and then. The PAs while still running were pulling secondary trains and the E8s served their lives pulling trains on the eastern side of the Santa Fe system where grades were not much of an issue. The Santa Fe preferred four axle power to pull their passenger trains on routes with steeper grades.
As to 3rd Rail vs. Atlas models you are looking at two different models based on how the drive is designed. In full disclosure I consult for 3rd Rail so I have an obvious bias towards their product, however I have never been disappointed with an Atlas product. As the 3rd Rail F7s are completely sold out, Atlas will be your best option for a prototypical train. However, if you are not as concerned about prototype power, the 3rd Rail locomotives are very high quality. The drive runs extremely smooth and they run down to nearly 1 smph without command. My 3rd Rail ATSF FTs are the finest diesels I own. Some new innovations that will really increase the running qualities of the 3rd Rail product include ball bearings on the drive axles starting with the SD7/SD9s.
One caveat for you is that due to the nature of the design of the horizontal drive, the high end speed of a 3rd Rail locomotive is about 60 smph. I find that to be plenty fast for my operations, but others do have a concern with that as the EL Cap did run 90 mph on the flat and straight sections of the ATSF mainline.
Having said all that, I have been a huge fan of Atlas locomotives for sometime. I believe they make a very high quality product and the F7 project looks like it will be a very nice release for them based on the improvements over the F3/F2s they have been producing.
Finally I have run my El Capitan / Super Chief on my club layout up to 18 cars with 11 being the El Cap cars. I pull it with two MTH FP45s since my F7s are PRR and 2 rail. While I am surprised how light the cars are for their size, with the LED lighting there is a lot of amperage left to power motors in the locomotives and you will want multiple powered units to pull the full train.
Best of luck in your decision making!
