Yeppers! It's one of those "I should have thought of that" ideas. I didn't read all 27 pages so if this was discussed I appologize...
First of all, I think the reason so much heat is retained by the bottles is mostly due to the closed lid. The water vapor can't escape and pressurizes the bottle. This pressure prevents any new vapor from being created. Since
evaporation uses heat energy, preventing the hot water from evaporating away causes it to stay hot much longer. Therefore, filling the bottle as full as possible should cause it to retain the most heat.
I personally use stainless steel water bottles. I can boil right in the bottle for cooking, and they hold the heat much much longer than plastics or aluminium. Yes, they weight a few ounces more but I consider the multi-functional aspect good weight.