Timebox for investigation; potentially can be solved with documentation.

If a info.magnolia.module.dependencies.field.DependenciesFieldDefinition specifies info.magnolia.module.dependencies.field.ReferencesDefinition that contains a list of ReferenceProperties, those are not used at all. Instead, the resolution of dependencies falls back to the deprecated list specified in the module config.

The culprit  is this line of code, where the references are not passed in from the ReferencesDefinition.