I kind of always figured Nightseer was what happened to Twilight Sparkles body. Which is why there never was a Twilight when the Goddess was destroyed and they all had there original personality's back.
Yes, but the minds of the original body always take sway. The Alicorn loses Twilights Cutie Mark afterwords replaced by another. She just temporarily used that body for a short period of time before dying. Plus different storys now have the Alicorn become Lacunae or some other Alicorn. I think Twilights body was killed at some point, either Nightseer or the one in Canterlot who figured out how to change the Dragon blowing out the Pink Cloud into a mouse.
Not sure about it, is it ever actually stated in the story? Might have to go back and look as its stated there minds were fused with Trixie/s being dominant. But I don't think they ever mention there body's. Besides, Twilight was one of the last Pony's in the facility to be pulled into the vat. Several other survivors were pulled in before she was.
Twilight was trapped in a safe room, one strong enough to survive the Balefire bombs. She could even watch other Pony's get dragged in on the camera's and hear there screams and pleading for mercy. She was one of the last to be pulled in and only after Trixie ripped the door open to get to her. Looked it up today.
Remember that the Alicorn's were rebuilt Pony's by the Goddess with there minds overwritten and controlled. When that control was loosened they began to regain memory's or develop quirks. Like Nightseer who was quirky, one Alicorn who told another that she remembered being a stallion and others. It seemed to happen when they were out of contact or something interfered with the Goddess's control.