To pack some resource files into a nuget package, what one would normally do, is the following.
Put all
Since NuGet currently does not support this out of the box your options are either to use PowerShell or to use a custom MSBuild target.
PowerShell
You should be able to avoid the project reload prompt if you use the Visual Studio object model (EnvDTE). I would take a look at Project.ProjectItems.AddFromFile(...) to see if that works for you.
MSBuild target
Typically the custom .props and .targets are used to customise the build process. However they are just MSBuild project files so you could add items for your resources into these project files.
Note that .props are imported at the start of the project file when a NuGet package is installed, whilst .targets are imported at the end of the project.
Customising NuGet
Another option, which would take more work, would be to modify NuGet to support what you want to do.