I love this question because it is about one TRADITIONAL villain of children's literature (Long John Silver) and one NONTRADITIONAL villain of "children's literature" ("the man upstairs"). (I put children's literature in quotes here because I don't consider The Bunker Diary part of true children's literature, but as a part of a new genre of Dystopian Children's Literature in league with The Hunger Games.) 

Let's look at Long John Silver first.  The original mutinous pirate, Long John Silver holds the record for most famous children's literature villain in my book.  Seeming to be a legitimate businessman who owns a pub, Long John Silver signs on as a simple cook on the Hispaniola.  Little does Jim Hawkins know that Long John Silver is a successful pirate who has lost his leg through his piracy! Eventually, Long John Silver describes himself quite adequately:

There's never a man looked me between the eyes and seen a good day a'terward.

Selfishness and greed and betrayal are a few of the qualities of this villain who is able to manipulate any situation by changing his own tune.  Keep in mind the original title for the work was going to be The Sea Cook, ... the incredible villain of fantasy was ALMOST the main character.  Of course at the end, Long John Silver does NOT get the treasure (Jim does) and is never seen again!  Good wins!

Now let's compare Silver to the villain of "Him Upstairs" that you mention in your question and is traditionally known as "the man upstairs" by Linus and his mates down in the bunker.  Both Silver and "the man upstairs" are villains, yes.  Long John Silver, though, has a motive:  greed.  THAT is why he wants the treasure.  "The man upstairs" plays horrid games with the people he kidnaps and NO ONE KNOWS WHY. He tries to get the prisoners to kill each other.  He tries to poison them.  He sends down vicious dogs.  He sends down drugs and alcohol.  Of course, at one point, "the man upstairs" simply leaves.  Does he simply get tired of the games?  Has he abandoned his prisoners?  Has he died?  NO ONE KNOWS. Finally, we can conclude "the man upstairs" is pure evil and yet does NOT get his comeuppance!  Good does NOT win in that all the characters die, including the narrator!

Thus, we can conclude that where Long John Silver follows both history and tradition in regards to villains, "Him Upstairs" does not.  And, although just as conniving, does not get his just desserts in the end.