We are actively working on a new release of Jetpack which will remove the upgrade prompts and help make it more clear that these suggestions are from Jetpack and not the directory. It should be out today or tomorrow.

As you reported above we have PR’s moving now and should see a release shortly. Our primary goal here is to help users and to prevent confusion, which is why I am excited to see Joost’s and other recommendations on how we can better communicate feature availability to users.

We will gladly update Jetpack to accommodate or use a better solution when and if that becomes available. I think we have a lot to share on the matter as well. There are a great deal of users across the web that experience WordPress through curated installations, or are unfamiliar with the details of how plugins work. All too often users end up installing several plugins to solve a single problem because they are unfamiliar with what to do next, where settings live, what features are packaged in a plugin, etc… These feature hints help to solve this for them, and if it’s a catalyst for core solution then all the better.