I'm going to harp on the torch-as-magical-light issue for a moment.
While it's certainly a valid means to achieve an effect, it makes me wonder: if we're coming to the point where the simulative mechanics have absolutely nothing to do with what we're using them to simulate, why bother with them at all?
To be a little clearer, if the answer to everything if "Well, you can take this mechanic for achieve X, and refluff/retool/warp it to fit Y," then could it be that we have the wrong mechanical divisions to start with?
I can think of at least two other ways to approach the problem: effects-based simulation mechanics, and narrative mechanics, neither of which have this problem.
Effects-based mechanics, like seen in M&M (and, I would say, creeping in d20 Modern with the attribute-based classes), use mechanics to model end results, not means. An M&M character might have a power to let him fly, without saying anything about how or why he can fly. Personally, I think d20 Modern channels some of the same philosophy (if not the implementation details) with the generic classes: a character is strong/fast independent of whether he's a martial artist or a swashbuckler.
The other option is fully narrative systems. To go to the extreme, you have something like Amber Diceless or The Pool, in which the mechanics don't try to model the game world at all, but just serve as an arbitration mechanism to decide which player gets to decide what happens next (at least when they disagree).
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At any rate, where I'm going with this is that I think we need to accept that different people have different creative agendas in the game.
For some, it's just an arbitration mechanism to tell a cool story, and for them refluffing/reworking/warping the mechanics to reflect what they want may be fine.
For others, it's a mechanism for simulating a fantasy world, and for them having mechanics that aren't rooted in the simulation may break their sense of immersion.
And for yet others, it's a tactical combat game, and none of it really matters as long as the combat system is fun and (relatively) balanced.