I noticed something weird in microsoft.dotnet.arcade.sdk\1.0.0-beta.20215.5\tools\Build.proj:

NuGetRestoreTargets is set to:

      <_NuGetRestoreTargets>$(MSBuildToolsPath)\NuGet.targets</_NuGetRestoreTargets>
      <_NuGetRestoreTargets Condition="'$([MSBuild]::IsRunningFromVisualStudio())' == 'true'">$(MSBuildToolsPath32)\..\..\..\Common7\IDE\CommonExtensions\Microsoft\NuGet\NuGet.targets</_NuGetRestoreTargets>

As far as I can tell, the MSBuildToolsPath is always:
MSBuildToolsPath = C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\MSBuild\Current\Bin

In regular builds it is set like this in Microsoft.Common.CurrentVersion.targets:

    <NuGetRestoreTargets Condition="'$(NuGetRestoreTargets)'=='' and '$([MSBuild]::IsRunningFromVisualStudio())'=='true'">$(MSBuildToolsPath32)\..\..\..\Common7\IDE\CommonExtensions\Microsoft\NuGet\NuGet.targets</NuGetRestoreTargets>
    <NuGetRestoreTargets Condition="'$(NuGetRestoreTargets)'==''">$(MSBuildToolsPath)\NuGet.targets</NuGetRestoreTargets>

Basically NuGet.targets is never in the same directory as MSBuild.exe as far as I can tell, so Arcade sets it to the wrong location. I don't know why it's currently setting it to $(MSBuildToolsPath)\NuGet.targets but it should probably just remove this line and always set it to $(MSBuildToolsPath32)\..\..\..\Common7\IDE\CommonExtensions\Microsoft\NuGet\NuGet.targets?

My repro: I was building Roslyn.sln with a path set to custom MSBuild:

1. git clone https://github.com/dotnet/roslyn
2. restore
3. In a regular command prompt (with fresh environment):

    set PATH=C:\roslyn\.dotnet;C:\msbuild\artifacts\bin\bootstrap\net472\MSBuild\Current\Bin;%PATH%

and it failed with:
import not found C:\msbuild\artifacts\bin\bootstrap\net472\MSBuild\Current\Bin\NuGet.targets

However I have to say that the failure is not deterministic so I was unable to reproduce since. Just wondering how it works though.