But the film clearly states that a green flash is for a return of a soul to this world -- not the other way around. There is no green flash when Will, Liz & Co. cross over to the other side, right? So a green flash can't mean that it's a sign of passage between worlds.
If it doesn't indicate life, then Jack isn't really alive, right? He's just sort of a zombie thing. Green flash is when a soul returns from the dead to this world.
That opens up a whole can of worms fanfic-wise. 😉
Remember Will offers to free his father from the Dutchman. The green flash as Will is leaving is probably from the souls of the crew that he releases.