It turns out that making an inverted mask (or a "clipping mask") in PIXI would be really difficult.  I'm not sure how to move forward with the clipping mask for the beaker (hiding the parts of energy chunks hidden by the blocks inside the beaker), so I'm just going to go on without it for now.
Working on the thermometer views and also made the initial energy chunk distribution a lot faster by not triggering events on energy chunk changes.