Avoid ngen for `amd64\` folder DLLs

We should not load assemblies from the `bin\amd64` subfolder of MSBuild in normal operation--VS, MSBuild.exe, and MSBuildLocator should load the single copies from `bin\` instead.

Some tools load MSBuild assemblies directly from `bin\amd64` and as a result we've had to ship should-be-redundant copies of assemblies there in several cases. We should avoid this where possible.

Today, most of those assemblies are marked for ngen, and further with the default ngen that uses `vsn.exe.config` (the in-VS binding redirects) AND FURTHER for all architectures:

https://github.com/dotnet/msbuild/blob/a71903d9684e24db3db261b27ca73c0ef879cf81/src/Package/MSBuild.VSSetup/files.swr#L180-L190