I have the same desire but I think there is no way of accomplishing this with only using npm tooling. Another script/tool could be used to arrange your package.
Alternative Solution
Currently I am copying my package.json into the dist folder and then running npm pack inside the dist folder. I think this essentially provides the desired arrangement of our package.
Here is some relevant reading on this npm design: Why no Directories.lib in Node.
It’s also interesting to note that jspm DOES respect the directories.lib option in package.json and rearranges the files when resolving the npm package. This all has come about for me because I am wanting to build a common library which can be consumed by jspm or npm/webpack.