TypeScript: MSBuild: Compile task output GeneratedJavascript does not match tsconfig.json or project settings

In the typescript targets:

    <VsTsc
      ToolPath="$(TscToolPath)"
      ToolExe="$(TscToolExe)"
      TSConfigFile="%(ConfigFiles.Identity)"
      YieldDuringToolExecution="$(TscYieldDuringToolExecution)"
      ProjectDir="$(ProjectDir)"
      ToolsVersion="$(TypeScriptToolsVersion)"
      TypeScriptCompileBlocked="$(TypeScriptCompileBlocked)"
      ComputeOutputOnly="false">

      <Output TaskParameter="GeneratedJavascript" ItemName="emittedFiles" />
    </VsTsc>

The output parameter GeneratedJavascript includes a js file for every ts file in the project even if:

1. The file is not set to TypeScriptCompile.
2. The file is excluded or not matched in tsconfig.json.

Side affect is publish fails trying to copy files that do not exist.