I have an aluminum seat post, so it's not a problem for me.
My experience is that the clamping danger is that the carbon material (and aluminum too) is extraordinarily thin (al bikes ... almost beer can thin) at the center of the top tube where you might be inclined to clamp your bike. Seatposts (at least the ones I am familiar with) are not butted, and not nearly as thin. I've not heard of anyone damaging a seat post with a stand clamp, so I'd feel comfortable just clamping to the seatpost, but being careful about it.
YMMV, of course.
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