The following entries were missing and I added them manually and the world got peace!
1: <SafeControl Assembly="Nintex.Workflow.ProjectServer, Version=1.0.0.0, Culture=neutral, PublicKeyToken=913f6bae0ca5ae12" Namespace="Nintex.Workflow.ProjectServer.ServerControls" TypeName="*" Safe="True" SafeAgainstScript="False" />
2: <SafeControl Assembly="Nintex.Workflow.ServerControls, Version=1.0.0.0, Culture=neutral, PublicKeyToken=913f6bae0ca5ae12" Namespace="Nintex.Workflow.ServerControls" TypeName="*" Safe="True" />
3: <SafeControl Assembly="Nintex.Workflow.ServerControls, Version=1.0.0.0, Culture=neutral, PublicKeyToken=913f6bae0ca5ae12" Namespace="Nintex.Workflow.ServerControls.WebParts" TypeName="*" Safe="True" />
If you have any questions you can reach out our SharePoint Consulting team here.