Eh, you don't get the point. Sure you can build some sort of a file explorer DS homebrew (which I believe already exist), but it won't help you changing the way the 3DS reads game cards. I don't know how else to explain. At the risk of repeating myself, you need a fucking way to run signed code.
I think the point is that you could use the DS homebrew to set the partition, or file offset, or whatever. The card obviously already "changes how the 3ds reads game code" since it redirects to a microsd. Surely you can redirect it to q different part of the microsd.
Edit Double ninja'd, lol. But the point still is you could do it in DS mode. You could even have 2 cards in the cart if nothing else.