Several years ago the company Brunton was the USA distributor for Optimus stoves. At that time they marketed a 0.6 liter fuel bottle that fit a normal bottle cage perfectly. That bottle however is no longer sold. I do not know if Optimus, Primus, MSR or an of the other stove bottle makers have such a bottle.
In the first photo you can see I carry my fuel bottle up much higher on the seat tube where it collects less road grime.
In my case I had the opposite problem, the bottle cage mounts were higher than I wanted not lower. But you might be able to modify my solution to fit your situation. The Long Haul Trucker has the bottle cage brazeons under the down tube mounted much higher. So high that it is hard to fit a large bottle in a cage located there. So, I took a piece of steel bar stock and drilled three holes in it. The uppermost hole is used for a bolt into the upper frame mount, the middle hole is for a bolt in the upper bottle cage mount and goes into the lower frame mount, the lowest hole is used for the bolt in the lower bottle cage mount. I also had to bend the bottle cage slightly to clear the chainrings.
See second, third and fourth photos. I also use a velcro strap to make sure that the bottle can't slide part way out and cause a problem with steering.
