I don't have the charts in front of me but I think this node of the decision chart is asking about bases required for restricted paths....e.g. the need for a base in Corcyra to allow land units to get to Sicily, or a base in Corinth for naval units to cross to Naupactus.
And on a side note, from your example, assuming you still have two Athenian bases in Athens, Phormio has to leave two naval units in Athens, one for each base, as per the decision chart footnote......an instruction which applies only to the city state theatres and only to Phormio (the solo player is free to empty a theatre of units if he desires).
Thanks Brent, that is what I was thinking it probably was referring to.
Also, thanks for catching my other error of Phormio needing to leave one unit for each base. I had missed that.