In Super Paper Mario
Stepping outside of The Thousand-Year Door, the 2007 sequel Super Paper Mario features Vivian on one of the in-game collectible Catch Cards. The English-language version continues to use feminine pronouns: “It’s Vivian from the last Paper Mario adventure. She was a great friend once she split from her sisters.” The card’s totally different description in the Japanese release gives more detail: 「どうじょうした マリオのなかも 火の魔法を 使う キュートな オトコのコ カゲ三人組という てきの一人だった」This text uses no pronouns but calls Vivian キュートな オトコのコ “a cute boy” or “a cute otokonoko,” understanding the character, then, as a crossdressing boy.
I am aware of no further specific references to Vivian’s gender in the franchise (aside from feminine pronouns).