It's the fact that the score is handled within the game mechanics itself – so the way to get a high score is not just to play but to play with the goal of modifying R12 (so it points to a high value)
They could have easily made score be handled outside the game and you get a point per every executed statement within the time limit etc – but that would not be as fun
It's not a reference, it's just a really neat game mechanic. Normally the high score is guarded by the game and changes only if the game deems it fit to change it. In this game, because the high score is accessible within the game and you can execute arbitrary instructions, you can use that to modify the high score.
It's as if in a more normal game the high score was kept in a big chest somewhere in the game world and once discovered you can start messing with the contents of it all within the rules of the world itself.
Thanks for sharing, it does makes me miss DEFCON, maybe next year...