I was a bit irritated by this, too. They definitely seem like a tool to me. On a related note, I have a random kindness rainbow in my toolbox, but then I got a second which refused to go in - bug or change in categorisation?
You asked, and we delivered! Firefly jars are now flagged as tools, so they can be stored in toolboxes. Party at TRB4's place :)
Note: May take a little bit before the changes get pushed to the live game world, but the changes are done and ready to go, so they're coming very soon if they aren't in by the time you read this.