Pilot(s) - *Doing pilot pre-flight things*
Gate Agent - "Alright, gate's closed, you're all clear!"
Ground Crew - "Alright, baggage is done, you're all clear!"
Pilot(s) - *Done doing pre-flight things*
"Okay, let's get permission from air traffic control to start taxi."
I imagined that whether or not all the bags (or even passengers) made it was of little concern to the pilots.
Your imagined scenario has him waiting for the bags, though!
The pilot has to know what's happening with his plane (e.g. are all the bags loaded or not) and is the final authority on everything that happens with the plane, so it all just comes out of that.
