So with the new scion classes coming out on NA, I have one thing that's been bothering me. Will both Phantom and Etolie Ex-cubes be included in the Hero Ex cube section in the limited ex-cube exchange? Asking because I need to figure out what classes I should max to farm the class ex-cubes.

Yes. Those 3 will form scion class section. Later, Luster class will be included in this section too.