Selenial
I Choose Violence
As I said, it can be deciphered using the In Game Files. They're definitely dealt with one at a time, and the gif where they are not comes from a very early draft of the malachor ending mod, that was eventually updated to the correct way.
There is definitely a section of the script that calls for Atton to attack her alone, the fight is described as "short, quick, brutal" but this is before the party is dealt with. So it fits with that scene. It appears he flees after this, to either survive or die in the end of the game in the Exile's hands.
To be fair to the modders, the script is hard to decipher in terms of sequence of events, but the events themselves are incredibly clear.
My reading of this area would be the following:
[list][*]Party attacks Traya. She deals with each separately, Atton first though after attempting to ambush her.
[*]Atton flees.
[*]Atton bumps into Sion in the hall.
[*]Defeats or is defeated by Sion depending on player's controls. Regroups with the Exile's party after they're freed and meets The Exile in the core.[/list]