In a recent game I played the Nomad and used the hero which allows the flagship and any unit it transports to be activated even if it's already been activated. My question then becomes: can I pick up units with the flagship from systems that have already been activated? This does not only include fighters or GF along the way but also GF in the starting system that's on the ground?

My group opted to say no, so my plan was foiled since I had assumed you could. Would love an answer for this.

The wording on the card is:

”ACTION: Place this card near the game board; your flagship and units it transports can move out of systems that contain your command tokens during this game round . At the end of that game round, purge this card.”

So, yes...yes they can.