Current Query Layer Activity needs a URL or a Layer with URL to function. If a FeatureLayer doesn't have URL the activity doesn't work: 'url or layer input is required. layer must have a valid url property.'
Therefore Querying a layer which was created using the Shapefile upload function doesn't work using the Query activity.
Can you update the current Query Layer activity or create a new one to Query Featurelayers client side?
Another advantage might be for layers which have a URL is that a client side query performs better without the roundtrip to the server.