It seems that both the Scout and Penn Flyer sets come in both conventional and remote versions, with the Penn Flyer having no less than 8 different sets and configurations to chose from!
Which sets (with product numbers) are you comparing?

You can run new and old trains on new and old track; everything is compatible.
To run your old trains on the newer FasTrack, you would need to disconnect the newer power pack from the track and connect your older transformer in its' place.
The newer LionChief trains can be run on the older or newer track with your older transformer set to maximum voltage.

Larry