Yes, make sure the dynamic map service has visible=true. The AT widget will only add tabs for visible layers(applies for feature layers as well) In the sample config I posted you can change visible=true on PoolPermits to see AT widget including the feature layers.
The way configuring AT widget in AppBuilder works is that by default it shows you all the possible layers the widget would add, by unchecking the checkboxes it would actually write out <excludelayer> tag to the widget config. At 3.1 we added a way where you can exclude layers within mapservice as well: <excludelayer>mapservicename/sublayerid<excludelayer>