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At the start of 3rd accomplice placement phase, the 1st port is still vacant, but there's already a punt arrived there.. Can I place my accomplice there, just to gain that extra 2 pesos?
Yes. German rules only disallow placement on a landed punt. English rules allow placement anywhere. The designer preferred the German rules.
Keep in mind the difference between placing an accomplice on a ware (on board the punts) and in a Port or Shipyard space.
It doesn't appear that the rules were updated in the 2014 reprint on the basis of any correction by the designer or company, and those rules appear quite clear that as long as a Port or Shipyard space is available, an accomplice may be put there at any time during the accomplice placing round. So a sure bet most certainly can pay off on the 2nd or 3rd accomplice placing round:
"Port and shipyard spaces: At each port and shipyard space, there is an accomplice place. In addition to the punt placements, players may deploy their accomplices on any vacant port or shipyard space. As with the ware spaces on the punts, a player can deploy several accomplices on port and shipyard spaces, when they are vacant on his turns.
"The goal of this action: to have accomplices on spaces where punts arrive at the end of the voyage so the player can earn the payment shown above the deployment space."
Key words just "where punts arrive at the end of the voyage".
And the ware placement rules for punts shows the clarity by contrast, because in this case you CANNOT place accomplices on punts that have already arrived:
"Punts already docking at the port cannot take any new accomplices."
So YES for Port and Shipyard spaces and NO for Ware spaces (on punts).