Oh the lobotomy isn't to ensure Us is recruitable in ACT II, it's to ensure from a story perspective that it is truly permanently severed from any hive-mind.

Originally Posted by the Narrator
"The brain lifts from the skull, but you notice an opportunity - you could cripple the strange creature, making it more subservient should it prove a threat."

Unfortunately due to inconsistent rewrites between Early Access and full-release the lobotomy lost its true gameplay and story purpose.

  • During Early Access its actual purpose (which still holds today mind you) was to sever Us from the rest of the illithid hive-mind at the beginning of the game. This allowed the player to attack other intellect devourers and thralls without Us attacking the party because it was truly severed from the hive-mind (and thus would explain today why it's not following the Absolute when we meet it in ACT II).
  • In full release however the entire prologue section got drastically shortened and there's nobody to attack anymore from the illithid faction (other than that single neutral intellect devourer patrolling the thrall chamber). Yet without the lobotomy performed Us will still attack the party if they attack the intellect devourer.

[Linked Image from i.imgur.com]

Larian while rewriting everything either accidentally forgot or intentionally ignored this fact and made Us recruitable without the lobotomy, but had they maintained writing consistency Us should not be recruitable without the lobotomy being performed. This would from a gameplay and story perspective make actual sense then for the character, while the choice to perform or not to perform it would carry actual weight; either get a fully able Us as a temporary companion for the prologue or crippled Us as a potential freed intellect devourer later. The choice carried actual weight in terms of story and gameplay, which is why today it is a useless story choice that merely cripples Us with a permanent debuff.

But in the scope of the question being asked by the OP; there is no excuse for Us not to be in the epilogue because it isn't tethered to the Absolute, especially if the player lobotomized it to ensure it can never again be a part of any hive-mind at all. So it survived the battle, but Larian unfortunately forgot to include the character in the epilogue.