The culprit was Sir Charles, for reasons suggested above, with Villasenor as accomplice setting off the EMP.
The sides of the glass case were indeed chemically bonded to the base. The base was indeed fixed.
However, the TOP of the case had been cut to create a kind of hinged flap made of glass.
By maintaining a reasonably high gas pressure inside the container, the flap could be kept closed tight. However, once the lights went out, the air pressure was released, causing the flap to fall open, and allowing the thief to reach in and remove the Engine from above. Then, using a sticky material on their gloves, or a suction cup perhaps, they pulled the flap back up to reclose the case. They may have used some adhesive to ensure it stuck, but the repressurizing of the case would have been sufficient to hold it.