If I'm understanding your argument correctly, then I think you're still smuggling in an assumption about "unequal representation" that doesn't hold. It isn't inherently unfair to group votes in such a way that two groups get the same number of votes in some domain despite size differences between them. [0]
I think that's an assumption that needs argued for (and one that ignores powerful cultural, historical, geographical forces).
[0] I'm sure we could think of all kinds of situations under which people collectivize precisely because their numbers would be too small to otherwise matter. I wouldn't want to argue that such systems are in principle unfair (and I don't think you would, either).
Federalism is not.
Unequal representation is.
The former does not require the latter; the fact that the two are both present in through US system is the result of a deliberate choice to implement systematic selective disenfranchisement along with federalism, not inherent in the nature of federalism.