Ok, I'm going to back up a bit and tell you why I see this as a problem (and it's not a mechanical problem).
We've established that, through externalized narrative control and externalized supernatural aspects, a pure mortal can achieve supernatural ends (lighting a fire at range or from nothing, traveling to the Nevernever, etc). However what you're saying is if we internalize any of that there is a penalty.
Can you imagine if you came up with a really interesting character concept, that was essentially a mortal with a neat aspect tweak (my "Clotho's blood runs through my veins (barely)" is a great example), and this other player has the same concept but without the story behind the aspect (He's just got "Weird luck"). Would it not suck if your GM decided that his character (functionally the same but much less story) deserved the refresh bonus and you didn't? That's what I see here, it's an inequity.
I also see what people are describing as abuse of the concept, but there are two issues I have with that. One is that literally anything that you can do with a supernatural aspect, you can also do with a mundane or externalized supernatural aspect. Second is that it's the GM's job to be the voice of reason. You ask "What's to stop me from taking a bunch of unassociated supernatural aspects instead of powers?" And my response is: The GM! The GM should look at what you are doing and say "Hey, you are clearly trying to game the system, cut it out."
Again, I see an inequity and it bothers me.