Ya know, I have asked my self that same question many times. I have run 2 rail cars (all the weathered cars i sell on Ebay) on the layout to test out the compatibility, as well as my 80' overhead loop in the bar and gameroom. I have found that with my Gargraves track, "running trains" is not a problem on either layout, but operations wise, switching cars does cause a problem. The 2 rail wheels do not like "shoving" (being pushed instead of pulled) through the Ross turnouts, they always want to pick the switch at the frog and derail. Orignally I had planned to swap everything out, and just buy 2 rail cars when I could, but with the Gargraves/Ross combo, I just can't get consistent performance for incident free switching.
I have also run Kadee equipped cars in between cars with the claw in several spots in the train. You just have to make sure that the kadee equipped car/cars are plenty heavy (many Lionel cars need extra weight) as the truck mounted claw will derail the kadee equipped in curves. I use stick on wheel weights to load em up (slightly higher than the NMRA standard) and everything stays on the rail.
I've never used Atlas track so I'm curious as to how the 2 rail wheels act on Atlas 3 rail turnouts. The Kadee couplers make a huge difference in visual appearance IMO. Closing the gap between cars also helps in getting a better "spot" at the industries too. My ice house platform will now hold 4 full cars instead of 3 1/2.