Elite tokens are, for all intents and purposes, a pre-made Mk 6 token. Similar to the rest of the upgrade progression, Mk 6 tokens can only be applied to Mk 5 hulls.
For the Punisher Cruiser, the Elite token's primary value is as a status symbol. It offers a boost to sector speed and a massive increase in cargo capacity, but more than that, having an Elite Punisher visibly displays your dominance of VEGA Conflict. Reserved for only the best of the best.