As far as my understanding goes:

Calyx just barely escaped with his (completely digital) life. He's literally a program. Very likely his entire 'folder', for lack of better terms just barely escaped when the terminal exploded. His soul has already rejoined the aetherial sea or been consumed, depending on how soul cells actually work. (I'm banking on soul cells literally consuming the soul and destroying it, hence its inevitable unsustainability, but that's a different discussion.)

Regardless, he just jumped data drives. The black void is either the 'digital world' of said data drive, or just the implication of 'an unknown space', likely the latter, somewhere within Alexandria where he manifests his faux body to converse with the unknown ascian.

The black void I believe is also used in a few cutscenes with Urianger and ascians during ARR/HW, but I could be wrong.

The aetherial rift we see in both The Chrysalis and the midfight cutscene of Seat of Sacrifice is not where the 7.3 cutscene takes place. Both we, and ARR Minfillia both traverse into this space.