I would think the 3V (3.6-3.7) is a limit set by the battery technology. Why if it's gonna charge over the lightning contact it needs to be transformed to 5V. I'm afraid that the current phone designs will not allow for any other way.

Maye though one could go for 6V with dual battery cells, and then bring it down to 5V.

But that would more than double the risk for a faulty battery, and complicate the charging circuits that would need to balance the cells, and make sure it would not charge if one cell is broke. If balancing would fail the result could be fire and explosion.

So just the risk would have Apple not to opt for a 2 cell version.