i have attached the controller config from OP, since it seems steam handles the controller:// handler incorrectly (at the time of this post)
extract/place the .vdf in
/home/deck/.local/share/Steam/steamapps/common/Steam Controller Configs/<steamid>/config/<gamename>
<steamid> is your steamid folder, if you are the only user it should be the only one
<gamename> is whatever you named vintage story when you added to steam.
if you named it "Vintage Story" place is in the "vintage story" folder. if it doesnt exist, you can just create a folder with the same name as in Steam.
also, i would like to add, if you are doing the cross-save sync and hate re-logging in everytime on each device.
open these two files
%APPDATA%\VintagestoryData\clientsettings.json
and
/home/deck/.var/app/at.vintagestory.VintageStory/config/VintagestoryData/clientsettings.json
search for
"stringSettings": {
until the end "}". on mine, it ended in
"currentHandbookCategoryCode": "guide"
},
and make sure they both match to the last device you logged in.
if you last logged in with PC, use the PC's settings on the Deck's settings and vice versa.
3246456598_controller_config.zip