Everything you have said is correct in-setting. Cubes should have no physical way to output data to a brain. That the sepsitor works in defiance of this fact is why it is classified as voodootech, and also is sodding terrifying.
Sure, the usual cube can not output data to the brain, but a sepsitorized one can. (Still there has to be a read mechanic, as you can not alter the stored memory in a cube without reading it, that was my point about incremental backups won't work with neural networks.) And being sepsitorized does not reprogram the brain, but the cube. But the mind cannot tell the difference, and will alter over time, to adjust to the reprogrammed cube: Because the act of recalling is always an act of rewriting that memory. So that false memories from the cube will over time alter the brains memories.
Problem with this, we have no word in any direction at all. The worst situation would be mine: terrified, trapped in your body until, if you survive the battle, the CA applies the Sepsitor effects to the brain with whatever way they have for long term (because removal of the cube is possible, see Teutonic Knights), while the "best" scenario is as you say, the mind slowly realigning itself with what the cube forces. My point also goes with the simplest way I can think of: make the cube you have modified take control, with minimal physical modifications coming from the Sepsitor's attack. Making the cube be able to output to the brain would require more, and would simply suggest a nanotechnological level so far above that of the Human nations that the CA could do things like simply grafting mines or rockets to enemy ships (using camo'ed shas ships and troops) and let the grey goo digest the ship... Also, if the process of Sepsitorization were simple and easy, it would be used wildly against the human and tohaa, yet the most common ammo is still lethal bullets and plasma, and we should see some sort of in-universe alert if the CA were mass converting people.
New CC Tohaa unit/character with Simbiont Armour and portable Nulifier to face the Sepsitor aspects of the IE WE ARE HOLDING THE IE FOR CENTURIES!!!
I'm pretty sure our loyal Chaksa would volunteer to go against the CA without a Cube and valiantly face true death. [note: they already do]
Linkable, combobreaker with Ectros Vulkan, lewl Or something like pitcher but with Nulifier or Pheropitcher, will be nice and nasty, nastynicer
