Throughout making a game, there are countless times where I have to try out an idea to see if it works. Does placing this monster there make a fair challenge, neither too difficult nor too easy? Is this the right price to charge for this potion? Is this monster fun to fight, or is it just annoying?
For exactly none of these does it make sense to create a prototype separate from the actual game. My ideas only make sense in the context of the game. In order to create a working prototype from scratch, I would have to recreate the entire game.
Instead, I try to keep my game flexible enough so that I can quickly and easily try out ideas in the actual game.