I know nothing about the story/game you're talking about, but I think this is an important and common misconception, and fanfiction that addressed it directly might be worthwhile.
It shows up in a bunch of places in fiction. Grant Morrison's Invisibles and the Nobilis and Unknown Armies RPGs, I think. A particular bit is that something very much like the present-day real world shows up as a part of the greater reality, setting up the plausible deniability that the world might really be like the postmodern meta-reality described.
I'd love to see stories about a rigorous thinker in such a universe working out ways to exploit its ground rules.
I'm not sure exactly how much this would be a different from the regular Mage. As far as I understand, it's already all about exploiting the meta-reality thing using whatever trickery the mages come up with.
I'm not also so sure how doing the rationalist subversion would work in Mage, since its universe is a lot sophisticated about working in a nonrational way than regular naive fantasy works. You're basically up against an adult postmodernist instead of a child who believes in wizards.
Mage: The Ascension is actually fairly shallow. It places extreme importance on "paradigm" (cultural beliefs in magic) in spite of the fact that as a mage becomes more "enlightened" he gradually realizes that paradigm is window dressing. It buys into postmodern criticisms of science without understanding either science or postmodernism and buys into every conspiracy theory ever invented regardless of how much sense it makes. The heroes and villains are so single-minded, morally grey, and self-centered that it becomes impossible to care ...
I've been enjoying reading Less Wrong fanfiction, and I wanted to suggest another fandom that should have at least one rationalist fanfiction: Mage: The Awakening. It's a roleplaying game about "modern sorcery." My description can't really do it justice...