If you're in the closed beta, then this should be very easy to figure out (I'm not in, so I'm afraid I'll have to pass the buck). Here's all you need to do:

 

1) Create a character in a new save file

 

2) Give that character the Amulet of Life (a basic item of which there is only one copy)

 

3) Create a different character in the same save file

 

4) See whether you can give that character the Amulet of Life

 

5) If the answer to (4) is "no," then indeed, each save file is like one box

 

6) If the answer to (4) is "yes," then see whether you can play Bringandoom with a party that has both characters in it

 

7) If the answer to (6) is "yes," then each save file is NOT like one box

 

I wonder if the game will have a "disassemble" feature that allows you to "return a character's deck to the box," as it were. Then if you try to reassemble the character but unique cards exist in other decks, you get a warning and/or those other decks get disassembled. This will allow players to unlock the difficulty settings with Group A, temporarily "bench" that group to play on heroic/legendary straight with Group B, and then temporarily "bench" Group B when Group A needs to be brought back to unlock the difficulty levels for newly released adventures. This would solve just about everything! ... except Deekow's concern about the basic / elite banishing. Luckily, Obsidian has a while to go before they need to cross that particular bridge.

So in the physical game, there is no issue with any of the stuff in this thread, because by the official rules, you can only play one "game" with one box at a time

 

"in the physical game, there is no issue" and "by the official rules, there is no issue" are different statements unless players have 100% attendance, it absolutely comes up in the physical game.