Yep, you can use a wood burner with an aluminum pot. I do it all the time with my hobo stove and my Heinie pot to save on fuel carried. As noted above, the water acts as an heat sink, raising the thermal inertia of the pot vessel as a whole, as well as becoming an heat exchanger as it boils. The energy needed to transfer the water from a liquid state to a gas state carries away an wholeheckofalot (technical term) of heat, which then rises with the steam and transfers to the atmosphere around it instead of staying in the pot and raising its temperature. The fuel in an alchy burner does the same.
All that being said, if you let your pot run dry...well...Bad Thingstm tend to happen. I've melted MSR Groundhogs (made of aluminum) down to slag trying to use them as pot supports with my hobo stove. These days, I've moved over to sixteen gauge steel wire (had it at home, so no extra investment) as a pot support, and it gets pretty hot--under the pot, it will turn fairly bright red. Thus far (about six months), no weakening of the supports has been evident.
Actually the finickiness (is that a word?) of the distance between a pot bottom an an alchy burner is mostly due a balance between actual heat on the bottom of the pot versus thermal feedback to the stove (which causes the alcohol to burn more quickly, lowering the efficiency past a certain point depending on the stove). Anyway, that's one of the reasons that playing with these little steel and aluminum contraptions is so fun.