Life is a nightmare but here we are

"But Kevin had escaped, hadn't he? Somehow he'd left that bloody room behind at Edgar Allan and become this, and Neil wanted the same so bad he could taste it."

due to her unusual circumstances, Twilight was kept in one of Celestia’s towers during her upbringing, with the intention of protecting her from the prejudices of the ponies that wouldn’t accept her new form.

instead, her childhood was that much lonelier. she was allowed Spike for company, Celestia as a teacher, and visits from her family and Cadence. Other than that, the royal staff was limited in their interactions with her, to avoid gossip, which still spread anyway.

in moments of high panic, as a filly, twilight could explode with an insane amount of magical power - enough to convert living organisms into other objects, effect gravity, and possibly time, depending on how one sees Spike's situation - in the draconequus au, this happened, but no one was around to help her stop the magical outpour.

initially, in an attempt to control the magical outpour, her body tried to convert her into an alicorn, as her magical output was great enough to trigger such a transformation - but it was doing more harm than good, and wasn't FAST enough. she was releasing too much magic too fast, and and it was searing her from marrow to fur.

in order to save her life, the magic itself converted her body into something that COULD handle that amount of dense energy all at once.

twilight doesn't really remember this process in detail. it happened relatively quickly - a matter of minutes - and the raw magic filling her head gave her a sort of amnesia for the major details of the incident, so the horror came from waking up in a new body, not the pain proceeding it.