Dunno if the energists were supposed to be connected to the whole Atlantis thing at all. As for the ending, just think that Van used the energist as a sort of conduit for Hitomi's wish to return home or something.
The weird looking energist was likely a plot device that was originally meant to be important since the series was originally supposed to be 39 episodes long. As it stands its only purpose would seem to be sending Van, Hitomi and Allen to Zaibach in ep 18. And maybe releasing Van from the "injured where escaflowne gets damaged" thing.