Generally, Jaspersoft reports are designed in JasperStudio. During this process, the main Dataset ends up with a saved query string as determined by the designer. This query is then used by Jasper Studio.
Now, when the report is run, the Jaspersoft libraries require a query string to be passed (if a null is passed, it seems to be treated like an empty string). However, there is no way provided for the jasperstarter (CLI or API) user to request the default query be used and thus "behave like JasperStudio".
The issue then is to:
Provide access to the main dataset query string via the API
Use this to provide a default for the currently mandatory CLI options such as --json-query, --jsonql-query and --xml-xpath.