In my opinion the selection process is not very intuitive for the Analysis widget. If I choose a layer from the map all the features of the layer are used. If I use the draw tool it is not clear what is actually going to be used in my custom geoprocessing tool. I did not initially realize that the draw tool was going to do a selection either. I just tried it to see what would happen.
Please change the Analysis widget UI allow a user to select a layer from the map, then show the current count and tools to add/remove a selection, then update the count based on the selection and show the selected features on the map. Add settings to the Analysis widget to define the selection methods and which is the default selection method for each input GPFeatureRecordSetLayer.