The concept of "The mod version is far better" strikes me as odd, and I want to put my thoughts and emotions down somewhere to get a better grasp on why this tickles me funny.
Alright, first concepts. Games are not made to be fun, this is not their singular goal. They provide an interactive experience, much like how movies provide a visual experience. You interact with a scenario and get a feeling for how the mechanics work and the emotional impact of whatever story it has. Being fun makes it an enjoyable experience, but many experiences are made through dealing with frustration and difficulty. Overcoming tremendous obstacles is a pretty well-known experience to craft.
Notch comes from a history of crafting experiences that deal with difficulty, complex systems and exploration. He wants to makes games that convey these things to the player. Minecraft is sort of an oddity when it comes to this, as it includes some frustrating stuff and risky situations, but is overall relatively easy to survive in. Primarily because of the awesome tool of breaking/building the environment, which is an evolved mutant of a system made for building cool stuff rather than difficulty of use for overcoming obstacles.
Often people will suggest things that for some strange reason Notch is reluctant to do. His reasons being they don't fit the idea of what he wants the game to be. I sorta accept that he has a vision for how the game is supposed to play. We have heard ideas and hopes about how he would want to make the game and add to it, but we ultimately don't have a full view of what his vision is.
So when chests that share resources across different chests are added, they are added under the vision of how they want the game to play. If they don't want some combination system in play then fine, working as intended. They don't want such things because it doesn't fit in the game they want to make. And I'm fine with that, if I don't want to play that game I can always just install mods.