In the same way that there is an explanation for why the Organization XIII members can (the portals to darkness)
Maleficent actually uses the same means of travel as the other villains of the game - The Corridor of Darkness
After the destruction of Enchanted Dominion, Maleficent and Pete used the corridors of darkness to travel to other worlds, eventually ending up at Hollow Bastion, the former home of Ansem the Wise and the last remnants of Radiant Garden after a brutal Heartless attack, which would be the perfect fortress to serve as a new base of operations. There, Maleficent would find everything she needed for her conquest of the worlds, including a report about the Heartless by Xehanort under Ansem's name and the very Keyhole that would lead one to Kingdom Hearts once all the princesses of heart were gathered
To explain the Green Fire, @Frank is more-or-less logical to his comment of "Because it's Disney". In the Disney films, Maleficient's dark magic contains the green light and Disney more than likey wished to keep her eeriness portrayed.