I think the idea behind prototyping first is to save your time making graphics/music for a game concept that is not fun.
That is, if it doesn't play well with boxes and circles, it's not gonna play any better with shiny boxes and circles.
If you absolutely need the graphics in place to inspire you to write the code, then sure, go ahead. But it eats up valuable prototyping time that can be used to churn through mechanic ideas and test them.
The advice also doesn't have to relate to the whole game. You might have decided you are definitely making some kind of turn based RPG. But you haven't worked out the details. That's where you prototype. You try every combination and bizarre idea you come up with, you play it, and you pick what's fun and throw out the rest. Prototyping can be as focused or as broad as you want.
I think prototyping with placeholder art works for most games, but not all of them.
Prototyping gameplay is important for games where the gameplay is king and art/story/setting is something on top. But if your game is going to be a regular platformer and the cool thing is the art, or if you're making an exploration game, etc, you should probably start with mockups and then make the game.
That is, if it doesn't play well with boxes and circles, it's not gonna play any better with shiny boxes and circles.
If you absolutely need the graphics in place to inspire you to write the code, then sure, go ahead. But it eats up valuable prototyping time that can be used to churn through mechanic ideas and test them.
The advice also doesn't have to relate to the whole game. You might have decided you are definitely making some kind of turn based RPG. But you haven't worked out the details. That's where you prototype. You try every combination and bizarre idea you come up with, you play it, and you pick what's fun and throw out the rest. Prototyping can be as focused or as broad as you want.