Various users have reported that under Ubuntu, Steam auto-cloud saves are writing to their home directory rather than the .config directory path set up in the Root Overrides under the auto-cloud configuration backend. Here's a thread reporting the issue: https://steamcommunity.com/app/447120/discussions/0/3104640350817747875/
As far as I can tell, everything is configured correctly and there have been no reports of this incident in the previous 3 years of the game being released, so it seems likely that something changed in the Steam client.
Various users have reported that under Ubuntu, Steam auto-cloud saves are writing to their home directory rather than the .config directory path set up in the Root Overrides under the auto-cloud configuration backend. Here's a thread reporting the issue: https://steamcommunity.com/app/447120/discussions/0/3104640350817747875/
As far as I can tell, everything is configured correctly and there have been no reports of this incident in the previous 3 years of the game being released, so it seems likely that something changed in the Steam client.