#relationships

I didn't read everything in details (not enough time to be honest) but I leave this post as a note for people who might want to do something for that issue.

There is something that has not been implemented yet in the external entity API for entity queries: in StorageClientBase::testDrupalConditions(), there is currently no (or limited) support for complex filtering on fields using syntax with sub-fields (like it is the case here with entity references) or with '%delta' (eg. ->condition('tags.%delta.value', 'news'))). That might be the reason why it does not behave like other Drupal entities with references.

This sounds overly complicated. What about simply having a config tab for the entity that allows you do choose which fields are entity references? By default, it could translate the remote ID value into the Drupal entity ID, and use that to make the reference?

For more complicated values in the reference field, it could allow for hook implementations that provide a translation in code.