I think we're talking past teacher at this point my man. You seem to be making all my points for me now.
It would be a drastic change to the game for sure. I wasn't offering/supporting this as a change we should make now, but rather as an oddity that they didn't in the 2.0 build, and would be a nice thing to see in say ten years in a 3.0. At that point you might not even have the same Chop as you rebuild the whole game again anyway, so what token it references (or not) gets reworked then and your fine.
Again, making my same point for me, yes energy is different in how it functions. But first Ed saw epic have individual tokens assigned first to the ship, then distributed to it's cards. Charge tokens could have filled that same role if they had wanted to do that again. Thank goodness they didn't.
Even the current previewed energy could have been tracked with charge tokens(or a charge token spin dial, whatever) with no change. You could have flipped up multiple charge tokens on the ship at the start of round, then turned them back down to use the upgrades. Functionally it would have worked just fine, until they start interacting. Which is why they have to remain split. "Attack: spend one charge from your ship." Or,"spend up to three charges from your ship, then do X" Would have been all it took. Literally, just change the word and it still functions. Ironically Chop would have been the precedent here as he breaks the charge token restriction of 'on card only' that they generally have, as you point out.