I'm hoping I can get some input from other people about this.
Video:
I managed to do this in one of my runs recently and I've never had that happen before. Did I just get crazy good RNG for the boss and that was the result? It seems this can take off about 20 seconds from the run but I haven't had any luck reproducing this.

LOL what? So she just didn't do the final phase? That's awesome. I wonder if Frayzlo has seen this before

I've managed it once, not 100% sure what caused it but I have a few ideas.
From what I've gathered, the crystal explosion does a decent chunk of damage if the witch is close enough (at least it feels like it does)
So combining that with fast attacks I think it's possible to do 2 phases worth of damage in one phase, but the game can only move one phase at a time, which is why it still goes to phase 2.
So in theory, you're entering phase 2 while the witch's health is in phase 3 (if that makes any sense)
I'm guessing the script to end the battle overwrites the script to start the next phase, which is why it cuts out the last phase.
But yeah, from what I can gather, it's too do with those crystals