I imagine the warning for CF (and prob AL) frames are for those trainers which clamp the bottom bracket or other parts of the frame (fork, seatstay, etc). Some of those fork mount trainers really put a lot of force on the headset area, but it depends.

Rear skewer clamp models allow some lateral flexion similar to road riding (the clamp only holds so tightly, my trainer flexes a bit, the frame flexes). I'd guess that if you're trying to do a lot of sprinting and such on the trainer, you could be putting a little more stress on the frame laterally. The stress is in a similar location to normal forces put on the bike on the road.

I don't see how there'd be a greater risk for carbon frames over other lightweight materials (aluminum or ti).

While some people I know favor rollers, fluid trainers fill the parking lots at races (and race warmups do involve some hard efforts) and are a staple for winter riding. I've seen trainers kill tires easily, but *knock on wood,* I've never seen a trainer kill a frame.