I did a little research and could only find Alexis Arquette as the birth name.
In her father's obituary:
actor, musician, and puppeteer whose credits include the 2000 film Best in Show and TV's Seinfeld. He is the father of actors Rosanna, Richmond, Patricia, David, and Alexis Arquette. His father was the actor Cliff Arquette.
Since this obit is dated 2001, before Alexis publically transitioned, i can only assume that was always her name.
Also, the credits in Pulp Fiction list her name as Alexis.
By the way, aggies_2011, Alexis is a "she", not an "it".