It is unlikely that another stove would work as efficiently in the Caldera Cone system since the current stove was optimized for the cone height and thermodynamics.
Yes, the Cones have cutouts for the handles of the pot. Since most heat is trapped inside the cone, the handles stay cooler.
I suggest you make your own stove from a few soda cans, and also buy one of the Caldera systems. Like Ben said, it is like a Jetboil for alcohol cooking. Not as light as an aluminum foil screen and wire mesh pot holder, but much more stable and wind resistant than the foil/mesh combos I tried.
Some of the new cones are also available in Titanium so they can be used with wood, esbit, and alcohol. Not sure which sizes come in that material, I got my Ti cone for my SnowPeak Trek 900; a very useful size for one person, and big enough for two in a pinch.
Roger, sorry to not include this link until this edit; the Ti cones are here;