Legacy and Modern deck sharing a deck box
There is a simple solution for pretty much all concerns related to too many cards and not enough boxes, and it's easy to teach players…
Present your deck and sideboard.
Let's look at the IPG for 3.5. Tournament Error — Deck/Decklist Problem:
Bullet point #4 is “The contents of the presented deck and sideboard do not match the decklist registered.”
People run into problems because they generally don't present their deck and sideboard, so the deck and whatever is in the box default to “presented.” However, a player could formally present a deck and sideboard and short circuit problems with cards in a box. Here's how:
1) Open box
2) Take deck out of box
3) Take sideboard out of box
4) Close box
5) Indicate the sideboard is your sideboard
Tah-dah.
By taking the deck and sideboard out of the box and formally presenting them, the player separates those cards from whatever else might be in the box. Since the box is closed, the player clearly shows that he or she is in no way accessing anything other than the presented cards. And since DDL hinges on presented cards matching or not matching, the player can clearly state that the deck and sideboard as presented match (assuming they didn't make a traditional DDL error).
When I teach players this, i let them know that we prefer to have the box be only the matching cards. However, this does give us a methodology whereby players can adapt their behavior to meet the IPG expectations even if they have extra cards laying around.