With the latest version of NuGet (2.7 or above) you do not need to use the Enable NuGet Package Restore menu option if you do not want to.
The latest version of NuGet, when installed in Visual Studio, will automatically restore any missing packages when your build your project. It does this without needing to add any new files to your solution and does not use MSBuild. It is now the recommended way of restoring NuGet packages.
You can also restore from the command line using NuGet with a command line similar to:
nuget restore YourSolution.sln