I recently saw that I had a notification to update a package […] and I realized that my other open Atom window did not show the update available.
I believe the “updates available” status bar tile only does a check when the window is opened. A package you have installed must have published an update in the span of time between when you opened your first window and your second
You can manually trigger a package update check at any time from the Settings view:
Also, the helpful toolbar at the bottom works differently.
You’re correct: the Git and GitHub status bar tiles change contextually based on the project folders open in the current window. In fact, they also “follow” your open workspace item, so if you open a file in one project folder, it’ll show the branch selector and the changed file count from that project, and if you open a file in another one it’ll change to show the branch and file count from the other.