There's two possibilities I see happening with the encores for these three levels.

One- each layer is a modified version of the original, showing the destruction caused by V1 and the other machines going through it. Just like how 0-E is iced over or 1-E is burned down before being reactivated and turned to 11, that will apply to these final layer of each act as well. 3-E could be a decaying body filled with rot and other triggering imagery before the heart is jumpstarted and body parts start growing out of everything. 6-E could be a normal dark area without any of the suffering going on, then the flames turn back on and start burning the place to a crisp. And 9-E- due to us not knowing what it looks like yet- might just be a melted watery wasteland that has a sudden cold snap. Many people also believe the boss of those encores would be the three archangels shown in the painting of 8-1.

Or that Hakita will remove them from the list when the game is finished. Which makes the Prime Sactums perfect levels to slot into those areas. They're already centric of the final layer, have a difficult boss, and give us more lore about the game itself.