Firebaseの公式ドキュメントのどこにもなかったので残します。

AppDelegate.swift
func application(_ app: UIApplication, open url: URL, options: [UIApplicationOpenURLOptionsKey : Any] = [:]) -> Bool {
    guard let sourceApplication = options[UIApplicationOpenURLOptionsKey.sourceApplication] as? String else{ return false }
    // これは動かない
    if FUITwitterAuth().handleOpen(url, sourceApplication: sourceApplication) {
        return true
    }

    // これは動く
    if TWTRTwitter.sharedInstance().application(app, open: url, options: options) {
        return true
    }

    return false
}

以上

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