Inner builds lose custom toolsets when building programatically

### Steps to reproduce

Minimal repro located here: https://github.com/dfederm/msbuild/tree/inner-build-loses-toolset/src/Samples/InnerBuildToolsetLost

After building, run something like:
`"artifacts\Debug\bin\Samples\InnerBuildToolsetLost\net46\InnerBuildToolsetLost.exe" "C:\Program Files (x86)\Microsoft Visual Studio\Preview\Enterprise\MSBuild\15.0\Bin\"`

### Expected behavior
Output:
```
Build succeeded
Log lines:
MsBuildToolsPath for OuterProject.proj: C:\Program Files (x86)\Microsoft Visual Studio\Preview\Enterprise\MSBuild\15.0\Bin
MsBuildToolsPath for InnerProject.proj: C:\Program Files (x86)\Microsoft Visual Studio\Preview\Enterprise\MSBuild\15.0\Bin

Toolsets were the same
```

### Actual behavior
Output:
```
Build succeeded
Log lines:
MsBuildToolsPath for OuterProject.proj: C:\Program Files (x86)\Microsoft Visual Studio\Preview\Enterprise\MSBuild\15.0\Bin
MsBuildToolsPath for InnerProject.proj: D:\msbuild\artifacts\Debug\bin\Samples\InnerBuildToolsetLost\net46

Toolsets were not the same!
```

### Environment data
Using the latest version of Microsoft.Build.Runtime (15.5.180.1)