Comparative advantage explains how to make use of inefficient agents, so that ignoring them is a worse option. But if you can convert them into something else, you are no longer comparing the gain from trading with them to indifference of ignoring them, you are comparing the gain from trading with them to the gain from converting them. And if they can be cheaply converted into something much more efficient than they are, converting them is the winning move. This is a move largely not available to the present society, hence its absence is a reasonable assumption for now but one that breaks when you consider indifferent smart AGI.

The law of comparative advantage relies on some implicit assumptions that are not likely to hold between a superintelligence and humans:

The transactions costs must be small enough not to negate the gains from trade. A superintelligence may require more resources to issue a trade request to slow thinking humans and to receive the result, while possibly letting processes idle while waiting for the result, than to just do it itself.

Your trading partner must not have the option of building a more desirable trading partner out of your component parts. A superintelligence could get more productivity of atoms arranged as an extension of itself than atoms arranged as humans. (ETA: See Nesov's comment.)

A sufficiently clever AI should understand Comparative Advantage

And a sufficiently clever human should realize that clever humans can and do routinely increase the efficiencies of their industry enough to shift the comparative advantage.

It really doesn't take that much human-level intelligence to change how things are done -- all it takes is a lack of attachment to the current ways.

And that's perhaps the biggest "natural resource" an AI has: the lack of status quo bias.