I am able to reproduce this with native applications so I assume flatpak is not the cause.
This is still a feature that I would like to get. There have been several cases of non-steam games where it would have been convenient to just shut it down with a button combination.
Nothing extracted yet.
Your system information
Please describe your issue in as much detail as possible:
Demonstrative video: https://www.youtube.com/watch?v=ZS0ZGvDmQ3s
You can not use the long press STEAM+B chord to shut down non-steam games on the Deck. What makes this behavior odd is that using the STEAM menu and selecting "Exit game" works just fine.
I previously reported this on the Steam Forums https://steamcommunity.com/app/1675200/discussions/1/5057002258665786228/
Steps for reproducing this issue: