Yeah, I don't buy it. If the "ship" is just the actual ship card the energy tokens can only go there, if the "ship" is the card and all of its upgrades then you get energy tokens to charge everything (which I don't believe is the case).
Edited by ForgottenloreReversals
The ambiguity is around the assign statement. The number of tokens to assign is clearly the energy limit of the ship. But you could, in theory, assign the tokens however you want to any upgrade on the ship.
No.
Allocate Energy: The huge ship’s controlling player may remove energy tokens from his Ship card and place them on any cards with an energy limit that are equipped to this ship.
Energy on the ship is clearly different than energy on other equipment on the ship. That's how you move them from one to the other. Assigning to the ship is not the same as assigning to an upgrade on the ship.