Unrestricted deck editor marking the missing cards with an alpha or showing them in black and white /greyscale at the end of the deck looks like a good idea.
The code for a deck is exactly the same with our without having all the cards.
When a player wants to play against any opponent except sandbox, a deck validation occurs. If the deck has any missing cards, it's redirected to the deck editor, hopefully with a pop up saying "you have missing cards, mate" or something like.
The sandbox doesn't have this validation, and somewhere there should be a label saying that it has 0 entering cost and 0 reward, same as PvP.
I like the random PvP system like EtG has, as unupped or without restrictions. More options maaay be added with a huge playerbase.