Yes, at the present moment you still need to specify a name even if it gets ignored. If you find it cumbersome you can just ignore a group and throw all the reference layers in there for now. (that's what I do)

I've opened an issue for this to be fixed in a new script version, thanks for the suggestion!
https://github.com/EsotericSoftware/spine-editor/issues/512

The script is now fixed! Please redownload it from this page: spine-scripts/photoshop at master · EsotericSoftware/spine-scripts