Thank you @j-loscos, works like a charm. I slightly adjusted your solution to include some new-lines (and removed the unnecessary restore at the end).
<Target Name="DisableWarnings" BeforeTargets="CoreCompile">
<ItemGroup>
<AutoGeneratedFiles Include="**/*.Designer.cs" />
</ItemGroup>
<WriteLinesToFile File="%(AutoGeneratedFiles.FullPath)"
Condition="!$([System.IO.File]::ReadAllText(%(AutoGeneratedFiles.FullPath)).StartsWith("#pragma warning"))"
Lines="$([System.String]::Concat("#pragma warning disable 1591",$([System.Environment]::NewLine),$([System.Environment]::NewLine),$([System.IO.File]::ReadAllText(%(AutoGeneratedFiles.FullPath)))))"
Overwrite="true"
Encoding="Unicode" />
</Target>