Was this ever solved? I too am having the same issue where I'm able to manually specify an embedded field in an entity index directly via the XML mapping, however, I'm unable to do this via Skipper, so I have to manually make the change after every export.
Further to this, where I actually want to create the index is in in a child entity, where the parent entity contains the embeddable. Either way, even on the parent I'm unable to create this index via Skipper whereas it works in Doctrine ORM XML mappings.