It’s probably because ‘jsDep’ kind of dependency does not map any of the maven dependency scopes. Take a look at ‘dependency mapping’ section in the user guide - you can configure the mapping between Gradle configurations and maven scopes.
Dependencies of custom configurations extending ‘compile’ don’t count as (Maven) compile dependencies, just as compile dependencies don’t count as runtime dependencies (although runtime extends compile). You can either add the dependencies directly to ‘compile’, or mess around with configuration-to-scope mappings (mentioned above).