I found out whats happening and honestly, Im feeling pretty dumb and kinda surprised.
Apparently, the visibility of certain apps is dependent on the PATH you take to get to the list of Reports, Alerts and/or Dashboards.
I was going into the Search app and then clicking on Alerts in the upper left top menu bar. Then I would click Apps: All expecting for ALL APPS to appear but launcher apps dont appear there.
When I went to Settings -> Searches, Reports, and Alerts... I found the missing launcher alerts and everything else.
Doh.
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