Not able to edit layouts with Wireless Horipad for Steam

[pigand]

The Wireless Horipad for Steam lacks functionality in layout editing during use in flatpak Steam (using the built in controller editing tools). The controller is unable to have the extra button mapping saved. Checked on a standard install of Steam and all features were present.

How it looks in the flatpak client when not working right, as not all buttons are accounted for in the legend.

I have tried enabling device=input in Flatseal and nothing changed.
edit:
extra info I have found is that the layout info uses a generic profile for xboxone controller listed as:
autosave:///home/complete/.var/app/com.valvesoftware.Steam/.local/share/Steam/
steamapps/common/Steam Controller
Configs/110351097/config/1189290/controller_xboxone.vdf

And it says so many times in the controller_ui.txt
controller_ui.txt

which is wrong and should just change to the custom layout named file, which it does in the standard client. Importing proper working layouts from cloud does not fix this either.