You're doing a deck check. Player A has 2 deck boxes on the table. Box 1 contains their 15-card sideboard. Box 2 contains tokens, dice, sleeves, and a couple of extra cards that would definitely be playable in the player's deck. What do you do, assuming no foul play?

IPG:

If there are extra cards stored with the sideboard that could conceivably be played in the player’s deck, they will be considered a part of the sideboard unless they are:
Promotional cards that have been handed out as part of the tournament.
Double-faced cards represented by checklist cards in the deck.
Double-faced cards being used to represent the back side of cards in the deck. These cards must not be sleeved in the same way as cards in the main deck and/or sideboard.

If the extra cards are in a seperate box from the Sideboard, then the would not be considered “stored with the sideboard”. Therefore there is no infraction. If you think that they might be cheating with having 2 “sideboards” then observe and/or speak with prior opponents for behavior during SBing.

Also : educate the player about the fact that MTR require to present their sideboard at the start of every match and let the opponent count it.
This is our best line of defense against sideboard shenanigans.

- Emilien

I want to clarify a bit more

The 2 cards are in the same sleeve as the rest of the deck. The cards are written on the decklist, crossed out but still easily readable, and the 2 replacement cards are written next to it.

The cards are stored in a deckbox containing tokens and dice, always present on the tabel next to the box containing maindeck + sideboard.

These are elements that are relevant for your investigation.
They aren't elements listed as relevant in the assessment of the penalty and fix in the IPG.

I get what you're trying to achieve, but don't forget that penalties and fixes are only two of the tools you have to catch and deter cheating. Investigation and education are other tools, and sometime more efficient. Dont rely only on one tool, and don't try to twist it too much to match your needs.

- Emilien

Here's a story:
Alex arrives at a tournament with his deck, but is unsure what the exact 60 cards will be. He's deciding what the last 2 cards will be. He even has all the cards sleeved, so he can test out the different versions. After writing out the decklist, he changes his mind about what to play. He crosses out the 2 cards and writes in the other cards. Now he has to decide what to do with the extra cards. He remembers that judges have told him that he cannot keep those cards with his sideboard, so he puts them in his other deckbox (one with only dice and tokens).

Now, is there a different story, where Alex has the cards in the other deckbox, so that he can have 2 sideboards and hope that his opponents don't notice him taking cards out of both deckboxes? Sure.

If Alex is deckchecked, hopefully the judges will ask Alex some questions and try to determine if story #1 or story #2 is true (or maybe some other version). If story #1 is true, then there is no infraction. If story #2 is true, then they are cheating. As Emilien started, these are elements in your investigation.

As judges, we are constantly telling players that they cannot keep other cards with their sideboard. Please do not start penalizing players with Deck Problem infractions, when they are doing exactly what we have told them to do.

Shawn