I just bought one of these, same color, I'll be using straight DC till I can pick up an NCE starter pack so I have to remove and store the decoder, but I'll keep an eye out for that Atlas problem- bummer as I am planning to Use Atlas Code 100 switches and track for my On30 layout, Thanks for the heads up.
The Atlas switches come with a little extender tab that allows the motor to be spaced further from the track. Use those and it will clear. There are a couple of places that would be hard for me. However, an under the table Atlas machine could fix that. I won't be bothering because this Davenport won't stay on this layout.