I think this is the answer. I suspect the exhibit designers had a cool idea for a display, did a rough estimate of the area needed and then commissioned the exhibit builders to make the big metal-framed cube. Either they made an error in their calculation or the innate variability in the size of stacks of used bills threw it off. It's also possible the exhibit designer simply decided a bigger cube which filled the floor to ceiling space would be a better visual. Which would be unfortunate because, personally, the exhibit concept I'm more interested in is "$1M dollars in $100 bills fits in this area" not "Here's $1M in bills." The first concept is mildly interesting while the second is just a stunt.
Regardless of the reason it's off, I think it's most likely there's only $1M of bills in the cube. The folks responsible for collecting and destroying used bills tend to be exacting in their auditing for obvious reasons. So when the exhibit designers got $1M in used bills approved and released, that's exactly how much they got. It also stands to reason that they'd design the cube a little bigger than their calculated area requirement to ensure at least $1M would fit (along with some method of padding the interior) - although >50% seems excessive for a variability margin, so I still think it was an aesthetic choice or calculation error. Of course, one could do a practical replication to verify the area required with $10,000 in $1 bills.
Regardless, it's an interesting observation and a cool counting program to help verify.