Lol. But that would mean opening it! 
Just kidding, of all the LR releases that was the one I knew would get ripped open immediately.
Problem solved then! Just take the game out of the Collectors Edition box, and stick it in with the rest of the LRG releases! I got the Collectors Edition too, and opened it as soon as the post office delivered it. This is actually the first LRG release I've opened of all the ones I've bought so far. Mainly because it's the only one I didn't have digitally already.
Even if you didn't open it, you could still make an empty custom case to put with you others on the shelf, and just store the LE in a different place.

In fact, my OCD would insist on it.
Just curious, does it drive you crazy that the first game didn't have the LRG number on it?