All .wixproj's have an `<Import Project="$(WixTargetsPath)"/>` at the bottom and near the top a couple properties that set WixTargetsPath property if **not** already set. NuGet inserts the Import for the .props file at the very top, that defines a custom path for WixTargetsPath which results in the .wixproj using the tools in the NuGet `tools\` folder.

We tested this it works very well.