Yes, the movement controllers are inverted and yes I use Virtual Desktop, but that just projects whatever is on my computer to my headset. I would have the same issue if the headset were connected via the Oculus Link cable.
I'm not sure about Steam being open. I'm not that familiar with how VivePort works, doesn't it basically run games through SteamVR? If so, then I think SteamVR is open. I haven't tried to play TWD in a while because of this issue. I've played several other games through VivePort without any controller issues (The Room, Moss, Obduction)