Tower of Zot controller.

[Atamis]

You are correct, it's Varis' body part. If you take Y'shtola with you to Tower of Babil in Trusts, she outright mentions it.

Ahh this is good to know. I have never used the trusts at all myself. I guess if they're hiding lore in there I should do them atleast once.

[Yukijin]

Makes me wonder which other body parts are controlling the other towers. There are at least seven towers and limbs can only account for four of them.

I also wondered that but then I remembered that they had the means to make clones of Varis, so they could mass produce him in order to raise as many towers as they wanted to

[Denishia]

Aw, that ruins the mental image of Zenos butchering smaller and smaller pieces of his father's corpse after Fandaniel informs him 'that, no wait, my calculations are off, we need at least two more towers to gather enough aether'.

[Darkstride]

My initial inference was that they just dismembered Varis's body so Anima could project its influence through the tower network from Garlemald.

Did anyone read it differently? Should I research this deeper? lol

This is also what I gathered. They used Varis' body parts.

[vormela]

Tower of Zot cutscene:
Urianger: I believe we stand in the tower's beating heart. What sayest thou, Y'shtola...?
Y'shtola: I see it. Aether siphoned from the land runs up through the spire, flowing to a single point...
Y'shtola: This is the core we seek. Y'shtola: Yet something is...off. As large as this structure is, it siphons far more aether than is required to sustain it.
Y'shtola: 'Tis as if the core is feeding on the energy. Consuming it. I need to take a closer look...
Y'shtola: ...Curious. There is something there, embedded inside the core.
Y'shtola: A man's limb...
Estinien: This is what we came to destroy?
Y'shtola: Yes. If you would be so kind?
Alphinaud: And that should be the end of it!

Dinner cutscene:
Fandaniel: The people cried out for salvation, their earnest pleas─one might even call them prayers─a supplication united for the Empire to reclaim her former glory.
Fandaniel: And so their will did manifest, channeled through the corpse of none other than Emperor Varis himself!
Fandaniel: And lo, the savior was born! The embodiment of the Garlean spirit, their Anima!
Fandaniel: It calls to its subjects, compelling them to take up arms and fight.
Fandaniel: And just as the wealth and power gravitate towards the Empire's capital, so too does aether, from every corner of the globe!
Fandaniel: The towers with which you and your allies have been so preoccupied were created as an extension of Anima itself. An ingenious design...

Talking to Lucia in the followup quests after regrouping:
Lucia: Are you well enough to make your report?
Lucia: This “Anima” was summoned with the corpse of Emperor Varis? Does their depravity know no bounds?

Zenos in cutscene after fight with Anima:
Zenos yae Galvus: The final order issued by Anima to the tempered thralls.
Zenos yae Galvus: “Should the Empire fall, the world must share her fate.”
Zenos yae Galvus: Of course, Father lacked the conviction to give such a command. The abomination born of his flesh was but a puppet─and I the puppeteer.

ETA: I kind of saw it thematically as an extension of Fandaniel's sundering and how he felt used by the Ascians. I know that is story and not lore but it is what colored my views. I saw the arm being like stem cells and the Garleans, like parasite-infected insects, started assembling the pieces of the tower around this thing that grew out of Anima and the pieces of Varis. Anima has arms though. So I don't know. I wasn't sure, personally. Could be Raubahn's. XD

EDIT AGAIN: THANK GODS WE CAN ALL SLEEP TONIGHT KNOWING WITHOUT A DOUBT VARIS'S BODY IS THE BODY PARTS WE FOUND TO BE POWERING THE TOWERS. What comforting knowledge!!! Thank you!!

[RyuDragnier]

Found the exact quote she says as you enter the last part of the Tower of Babil.

Y'shtola: "As I suspected, each tower contained a piece of his corpse!"