If you're having hull problems I feel bad for you son, I've got 99 problems but a breach ain't one.
Does it create a virtual die that is a copy of another crew die which is then placed virtually on an appropriate station or threat? Or is this effect really like "Change a crew die" but only to a face of another die the player currently has?
It's more like your second interpretation.
Why would it create a virtual die?
Clearer rules are needed in this game.
Like the rulebook states: Copies the face of any other die rolled the same round
When writing rules, there is such a thing as too elaborate. You have to strike a balance between playability, intuitiveness, and concise.
Specifically the rule for Athena's commander action is a straight reproduction of similar rules found in much more popular games like Magic: The Gathering in which cards allow you to Copy the ability of any other card in play.
User experience designers seek to lower the barrier of gameplay by taking advantage of the way users are already primed to understand something (whether or not that something is syntactically correct).
The unique thing about solitaire games is, competitive games have a kind of self-policing subtext to the rules. For example, if you play a game where the winner is determined by the player with the most victory points at the end of a game, and a player has a card that says "Gain 1 VP" but it doesn't say "Then discard" you can technically keep playing that card until you have more VP than you can dream.
But that would clearly break the game. So there is some level of understanding how things function in order to provide order and pathways of fair gameplay. This aspect is much less clearer in solitaire games, especially when first learning them.
The verb choice of copy (athena) vs change (halcyon) is largely arbitrary from a rules standpoint. Players most likely encounter change first, and wonder why it copy isn't change when copy first appears. The important differentiator is the object performing the action.
Halcyon commanders are activated by placing them in the appropriate station, then you change a different crew die to another face.
Athena commanders themselves perform the function of another face, so long as it was rolled the same round.
So while you could make Athena say: change this die to the face of any other die rolled in the same round.
You could not make the Halcyon say: You may copy any available die.