I think the Goldeneye/Perfect Dark model is really cool but I feel it could in fact be expanded on into almost a sub game by splitting the cheats into two lists.
So say, one list must be done "pure" (no cheats running) but the other can be cheated towards making the order you unlock them rather strategic ala Megaman bosses. For example: You have to speedrun a stage that contains a large chunk where you retrieve extra expolosive ammo to clear a collapsed hallway - you begin with a single grenade so ifitine ammo becomes a prerequisite. Of course, Invulnerability would be the final cheat in that list, requiring practically all the others to even get a chance at it.