Ok after digging around a bit, and experiencing the same woes that you are describing. I believe this is what you are after:
Jquery boilerplate is a template for your jquery-plugin module layout. It includes both a package.json file for your npm repository publishing, and it includes a package.jquery.json file for uploading modules to the jquery module registry.
As for the answer that you really want. You are not going to get it... today. You could see that these package systems are written by different people at different times and solve the same problem. Thus the redundancy.
i.e. node.js and thus npm is a tidal wave that is coming in the community. However it is not the only way for you to use javascript pacakges and thus not the holy-grail of javascript package delivery... yet... Which is why jquery plugins registry needs to exist... today..
I feel compelled to point out that the npm repository is for javascript packages, where the as jquery packages one is just for jquery packages.
Finally:
You can see for example that maintainers is a attribute that jquery plugin registry is using in the community that node plugins is not using. ( there are some other attribute differences ) see:
Your question: does illustrate a valid point tho. There is redundancy in these two package repositories. Jquery packages should just use the package.json file format for its imports.