I agree that some things, like the weapon damage example, are just routine parts of a game. If they are adjusted, there ought to be a consistent way its done. One way is DR where certain types bypass the resistance, and the resistance and/or immunity works in the same application across the game.
Your doom die example seems consistent to me in that there is a process for the GM to make a monster explode on death. The GM understands it, and as a player I can come to understand it. However, if a GM is just deciding on a whim that X exploding monster does random damage, and Y monster does a different amount off of different conditions, then it gets into inconsistency territory. Where the rulings are more wild west then informed and guided by any system foundation, it becomes inconsistent.