Totally agree about this being an useful script!
I always wanted to update that script to a more integrated design. Great to see you did the work :) Hopefully @joeytwiddle will update his script. I couldn't find the script on his GitHub profile, so a PR isn't possible.
Before starting to write, I would thanks the creator of this awesome userscript, i searched for 30 minutes in GitHub settings but can't find something similar to this!
Anyway, the look of the userscript was ~ugly, so I decided to tweak it to make it more "user-friendly" (and with a better look!) so here's the modifier code (i only tweaked css and 3-4 lines of js, feel free to use a compare tool to see the differences ^^)
Here's the code: https://github.com/SkyzohKeyx/GitHub-Dropdown-Notifications :)