NuGet pack fails to resolve assembly when retrieving portable assembly metadata

[BladeWise]

Using nuget pack Sample.csproj -verbosity detailed over the attached project produces a System.IO.FileNotFoundException, trying to resolve System.Runtime, Version=4.1.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a.
Such exception is raised while trying to access assembly metadata in the reflection-only context.

The Sample.project.json file contains the following dependencies:

{
  "supports": {},
  "dependencies": {
    "Microsoft.NETCore.Portable.Compatibility": "1.0.1",
    "NETStandard.Library": "1.6.0",
    "NuSpec.ReferenceGenerator": "2.0.0-beta-bld14",
    "System.IO.IsolatedStorage": "4.0.1",
    "System.Reflection": "4.1.0",
    "System.Runtime.Loader": "4.0.0"
  },
  "frameworks": {
    "netstandard1.5": {}
  }
}

I am aware that packing from csproj while using project.json could not work, so the sample project could not produce a valid package anyway (see #3108), but this issue seems more general.