As it says in the Editor’s note, this chapter occurs outside the comic’s main timeline.  The caption at the top says it’s happening on the night of Halloween, 2018, but it’s also happening sometime before Chapter 11 (The Gathering).  So Colt and Junior are still very much alive.  So when does Chapter 11 (which began back in March) happen?  Sometime after Halloween, 2018.  Like most printed annuals, this issue happens sometime off to the side, disconnected from the main storyline, but still considered to be canon.  Really, don’t let it stress you out.   Just sit back and enjoy learning Tommy’s story!