The BaseLayerPicker is meant to be a simple widget for picking a base layer, that’s about it. You can also have an item in the picker include multiple layers, so that you choose a group of layers to add. However, we don’t have a ui for independently picking two separate layers at this time. More general configuration of data sources and imagery is taking place as part of the DataSourceBrowser widget effort, but we haven’t done anything at all with imagery yet there.
What you want to do is trivial from an API standpoint, so you have either add your own UI for selecting the layers, or hack up the BaseLayerPickerViewModel.js file to allow for the BaseLayer picker to “target” a particular layer index (base layer, layer 1, etc…).