It's not a "problem" per se if you are setting your project settings and configuration every run.
For instance Automation API relies on those files still being present because under the hood Automation API is still invoking the Pulumi CLI in whatever directory contains those files. But Automation API was designed with the idea that eventually it would no longer rely on the CLI, and would be able to invoke the Pulumi engine directly. Once that is possible it will no longer be necessary for those files to even be created on the file system.
So like I said, if your build is setting your settings & config each run it isn't necessary that you preserve those files.