The 'Extract Data' analysis tool does not honor the geometry of the study area if the output is set to CSV, KML, or shapefile.

Workaround

1. Share the map to ArcGIS Web AppBuilder, and add the Query widget.
2. Set up the query for the layer to be extracted.
3. Set the filter to 'Only return features that have a spatial relationship with features in another layer', and the spatial relationship to Intersect.
4. In the options, ensure 'Allow to export results' is checked.
5. Run the query to get the features which intersect with the reference layer, and export the results.

Steps to Reproduce