Hard-to-diagnose failure when deploying Framework MSBuild assemblies but intending to target Core

### Steps to reproduce

1) Build MSBuild
* (`.\build.cmd /p:CreateBootstrap=true`)
2) Deploy it
* In an admin command prompt, run `powershell.exe`, then `scripts\Deploy-MSBuild.ps1`
* Specify the location to the folder used by `dotnet build` (typically under Program Files\dotnet\sdk).
3) Run `dotnet build` on anything.

### Expected behavior

Some indicator that you built targeting Framework but tried to run MSBuild as if you'd targeted Core.

### Actual behavior

Build Failed
0 Warning(s)
0 Error(s)

[msbuild.log](https://github.com/microsoft/msbuild/files/4325429/msbuild.log)

[msbuild.txt](https://github.com/microsoft/msbuild/files/4325437/msbuild.txt)
(Change the latter to a binlog)

Since this won't affect external customers, we shouldn't make it run every time someone builds. It might be reasonable to take the location and output a warning if running `Deploy-MSBuild` without specifying Core to a folder under sdk.