Thanks! I already have a valid manifest.toml:
# This file is machine-generated - editing it directly is not advised
julia_version = "1.7.3"
manifest_format = "2.0"
[deps]
but PackageCompiler defines valid as nonempty, and so your solution (adding a package) removes the warning. I now believe that it is safe to ignore the warning in my case because my code depends on no packages, so it is okay to have an empty manifest.