The theory proposed in "Chariots of the Gods" is indeed interesting, but...
Never forget that in "Raiders" the Ark is depicted as a strongly spiritual artifact. When Belloq opens it after the ritual at the end of the movie, it is clearly shown that things which seem to be ghosts/damned souls appear from its dephts to punish the Nazis.
So how can you explain the ghosts if you assume that the Ark is a technological alien device?
I personally think that even if this new movie will be centered around the "Chariot of the Gods" idea, the alien artifact won't be the Ark of the Covenant.