Alicorn Twilight is just a Variant of the original Twilight. Created during the battle of Arkus back in Skylands, separated from Twilight. Alicorn Twilight often spoke of Twilight as her sister, most variants speak of their originals like that.
(Its from my fan fiction where Twilight and Alicorn Twilight exist as two individuals. Twilight continues her work as a scholar with the gremlin alchemist, Pop Fizz. While Ali, (Twilight seems to call her that) happily married to the red variant, Punch Pop Fizz rules the Variant World side by side.