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If I understand correctly MetadataComponentDependency supports standard and custom fields on standard objects, but neither on custom objects. Will it eventually support standard and custom fields on custom objects as well?
It is my understanding that custom objects and fields are already supported by the dependency API.
Based the the title of your question, ensure you are using the Tooling API to run the SOQL query and that they API version is v47.0 (Winter '20) or higher.