I still had to kill Amalgams that spawned on previous phases in the final one, maybe one of those can get bugged or something? (ie: when the arena gets destroyed and they are standing on the bits that falls off).
I went with Hushed invi Loki and Rubico Prime (also may be related to other enemies on the fight being alerted?), if someone wants to try with that loadout
Will test a few more times after I finish all the planets (I'm not mad enough to fight this thing again today) to see if I can kill it consistently the way I did it today or if I also run into the bug, will edit this post if