In 100% With Fixed EMS you should have greatspin at this point and if you do you can 1 cycle both phantom zants. To do this simply stab him once then do 3 greatspins. If you only get 2 greatspins, you can just combo him next time round. If you only get 1 greatspin then next time do 3 slashes and a greatspin. The window is very wide hence 3 greatspins isn't hard.
In other categories it is possible to 3 cycle him instead of the 4 cycle method below and still without any RNG of waiting for Zant. To do this stab him then do 2 quickspins, repeat this for the 2nd cycle and for the final cycle do 1 slash then 3 quickspins to finish.
This strategy may not be perfect in theory however it eliminates all RNG from the fight and hence is best strategy. It does require you to be able to hear and locate Phantom Zant fast. The idea is that Zant doesn't teleport around the room until he spawns his first wave enemies, and if you don't deliver the final hit of the combo he won't start spawning enemies. Because of this we can stop him ever teleporting around the room by just doing 3 stabs for 3 cycles and then on the 4th cycle deliver the combo which will kill him.
In All Dungeons because you beat Temple of Time before Palace of Twilight and skip the grove cutscene Early Boss Fights is activated. However although the fight does start as soon as you enter and you can sometimes see him teleporting about this doesn't mean you can make use of it. This is because for the Phantom Zant in the west wing there is a cutscene after the door closes and when it is skipped the room is reset, similarly if you go to the East wing first it is impossible to bring the Sol back because the platform isn't there to raise you
By following the Quick Fight strategy in a slightly different way, it's possible to 1 cycle Phantom Zant in all categories. Note that this method requires three frame-perfect hits for an optimal fight. Instead of waiting on Phantom Zant to warp away and then going to him for the next round of attacks, by timing the first hit of each round perfectly you can interrupt that warp and defeat Phantom Zant without any warping. If your timing is off on starting the next round of attacks this will not work; early and you get an RNG fight, late and you miss. Because of this this strategy is generally not considered RTA-viable but it is here for awareness.