@kylebarron : In short... not really. :) Still works for me, and since there have been no issues (since I apparently never turned them on... oops!) had kinda forgotten about it.
In general it seems like Atom separately syntax-highlighting packages from execution packages, so I don't know that it's necessary optimal to roll everything together, but you are welcome to push anything you want to this, or if you create a better alternative, happy to delete/merge this like we did with syntax.