I bought mine from John Eaton who had customized it for a sub box as well. Didn't impact the ability to use it as a storage box - all he did was cut a hole in the back of the box for the wires to pass through. He may have had some internal mounting brackets to hold the sub, but if he did they were removed when I bought it.
Definitely don't trash it, if nothing else it can be measured for replication.