Since the recent update that added focus-related changes to the pop-out chat window I’ve been unable to play games with an Xbox Controller plugged in while a chat window is active, despite it being in the background.
Doing so without manually making sure the chat window has lost focus will result in me triggering a call to the person I’m chatting with since the only thing a controller can do with the chat window (besides interacting with buttons) is toggle between the call button and the chat box.
Edit: Correction, it can also close the chat window, apparently.
TL;DR: Pop-out chat window remains focused while in the background and takes controller input.
I do not have Microsoft Trio installed, but I’ll check out the thread you linked. It didn’t turn up in any of my searches for whatever reason, same goes for the actual bug report forum.