msbuild: PackageReference is not resolved while it works in Visual Studio

Steps to reproduce

• Create a Empty Web Application Project in Visual Studio.
• Make it really empty by removing the DotNetCompilerPlatform stuff
• Add a Nuget package reference to Microsoft.AspNet.Mvc version 5.2.4
• Add a Global.asax and its code behind with a using System.Web.Mvc
• Compile in Visual Studio
• Compile from the command line

Directory contents:

/
- Properties/
  - AssemblyInfo.cs
- Global.asax
- Global.asax.cs
- web.config
- Empty.WebHost.csproj

Empty.WebHost.csproj:

<Project ToolsVersion="12.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
  <Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
  <PropertyGroup>
    <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
    <Platform Condition=" '$(Platform)' == '' ">AnyCPU</Platform>
    <ProductVersion>
    </ProductVersion>
    <SchemaVersion>2.0</SchemaVersion>
    <ProjectGuid>{080CBD85-3B74-4ECC-8389-47E594F376DE}</ProjectGuid>
    <ProjectTypeGuids>{349c5851-65df-11da-9384-00065b846f21};{fae04ec0-301f-11d3-bf4b-00c04f79efbc}</ProjectTypeGuids>
    <OutputType>Library</OutputType>
    <AppDesignerFolder>Properties</AppDesignerFolder>
    <RootNamespace>Empty.WebHost</RootNamespace>
    <AssemblyName>Empty.WebHost</AssemblyName>
    <TargetFrameworkVersion>v4.6.2</TargetFrameworkVersion>
    <UseIISExpress>true</UseIISExpress>
    <Use64BitIISExpress />
    <IISExpressSSLPort />
    <IISExpressAnonymousAuthentication />
    <IISExpressWindowsAuthentication />
    <IISExpressUseClassicPipelineMode />
    <UseGlobalApplicationHostFile />
    <NuGetPackageImportStamp>
    </NuGetPackageImportStamp>
  </PropertyGroup>
  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
    <DebugSymbols>true</DebugSymbols>
    <DebugType>full</DebugType>
    <Optimize>false</Optimize>
    <OutputPath>bin\</OutputPath>
    <DefineConstants>DEBUG;TRACE</DefineConstants>
    <ErrorReport>prompt</ErrorReport>
    <WarningLevel>4</WarningLevel>
  </PropertyGroup>
  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
    <DebugSymbols>true</DebugSymbols>
    <DebugType>pdbonly</DebugType>
    <Optimize>true</Optimize>
    <OutputPath>bin\</OutputPath>
    <DefineConstants>TRACE</DefineConstants>
    <ErrorReport>prompt</ErrorReport>
    <WarningLevel>4</WarningLevel>
  </PropertyGroup>
  <ItemGroup>
    <Reference Include="Microsoft.CSharp" />
    <Reference Include="System.Web.DynamicData" />
    <Reference Include="System.Web.Entity" />
    <Reference Include="System.Web.ApplicationServices" />
    <Reference Include="System.ComponentModel.DataAnnotations" />
    <Reference Include="System" />
    <Reference Include="System.Data" />
    <Reference Include="System.Core" />
    <Reference Include="System.Data.DataSetExtensions" />
    <Reference Include="System.Web.Extensions" />
    <Reference Include="System.Xml.Linq" />
    <Reference Include="System.Drawing" />
    <Reference Include="System.Web" />
    <Reference Include="System.Xml" />
    <Reference Include="System.Configuration" />
    <Reference Include="System.Web.Services" />
    <Reference Include="System.EnterpriseServices" />
  </ItemGroup>
  <ItemGroup>
    <PackageReference Include="Microsoft.AspNet.Mvc" Version="5.2.4" />
  </ItemGroup>
  <ItemGroup>
    <Content Include="Web.config" />
    <Content Include="Global.asax" />
  </ItemGroup>
  <ItemGroup>
    <Compile Include="Properties\AssemblyInfo.cs" />
    <Compile Include="Global.asax.cs">
      <DependentUpon>Global.asax</DependentUpon>
    </Compile>
  </ItemGroup>
  <PropertyGroup>
    <VisualStudioVersion Condition="'$(VisualStudioVersion)' == ''">15.0</VisualStudioVersion>
    <VSToolsPath Condition="'$(VSToolsPath)' == ''">$(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v$(VisualStudioVersion)</VSToolsPath>
  </PropertyGroup>
  <Import Project="$(MSBuildBinPath)\Microsoft.CSharp.targets" />
  <Import Project="$(VSToolsPath)\WebApplications\Microsoft.WebApplication.targets" Condition="'$(VSToolsPath)' != ''" />
  <Import Project="$(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v10.0\WebApplications\Microsoft.WebApplication.targets" Condition="false" />
  <ProjectExtensions>
    <VisualStudio>
      <FlavorProperties GUID="{349c5851-65df-11da-9384-00065b846f21}">
        <WebProjectProperties>
          <UseIIS>True</UseIIS>
          <AutoAssignPort>True</AutoAssignPort>
          <DevelopmentServerPort>1983</DevelopmentServerPort>
          <DevelopmentServerVPath>/</DevelopmentServerVPath>
          <IISUrl>http://localhost:1983/</IISUrl>
          <NTLMAuthentication>False</NTLMAuthentication>
          <UseCustomServer>False</UseCustomServer>
          <CustomServerUrl>
          </CustomServerUrl>
          <SaveServerSettingsInUserFile>False</SaveServerSettingsInUserFile>
        </WebProjectProperties>
      </FlavorProperties>
    </VisualStudio>
  </ProjectExtensions>
</Project>

Global.asax:

<%@ Application Codebehind="Global.asax.cs" Inherits="Empty.Web" Language="C#" %>

Global.asax.cs:

using System.Web;
using System.Web.Mvc;

namespace Empty.Web
{
  public class MvcApplication : HttpApplication
  {
    protected void Application_Start()
    {
      AreaRegistration.RegisterAllAreas();
    }
  }
}

web.config:

<?xml version="1.0" encoding="utf-8"?>
<configuration>
</configuration>

Properties\AssemblyInfo.cs:

using System.Reflection;

[assembly: AssemblyVersion("1.0.0.0")]
[assembly: AssemblyFileVersion("1.0.0.0")]

Command line

msbuild .\Empty.WebHost.csproj /t:restore,Build

Expected behavior

The build should succeed in Visual Studio. The build should succeed on the command line.

Actual behavior

The build succeeds in Visual Studio. The build fails on the command line.

Build FAILED.

"P:\cy\apps\cam\src\Core\Empty.WebHost\Empty.WebHost.csproj" (restore;Build target) (1) ->
(CoreCompile target) ->
  Global.asax.cs(2,18): error CS0234: The type or namespace name 'Mvc' does not exist in the namespace 'System.Web' (are you missing an assembly reference?) [ P:\cy\apps\cam\src\Core\Empty.WebHost\Empty.WebHost.csproj]

    0 Warning(s)
    1 Error(s)

Environment data

msbuild /version output:

Microsoft (R) Build Engine version 15.5.180.51428 for .NET Framework
Copyright (C) Microsoft Corporation. All rights reserved.

15.5.180.51428

OS info: Windows 10 Visual Studio 2017 15.5.6