Ignoring the source of the fuel and oxygen, consider what happens if you do have a layer in the upper atmosphere that's constantly burning bright and hot enough to heat a nearby moon. The planet within is entirely enclosed in this shell of fire with no way to shed heat absorbed from it, and will quickly heat up to the same temperature as the flames. The end result is a ball of molten rock, and the annihilation of any biological activity that might produce fuel and oxygen.
Additionally, combustion can only release energy put into the mix of chemicals using a greater amount of energy from some other source. If that other source is radioactive decay/primordial heat, there has to be enough to produce that amount of heat regardless of any intermediate biology or chemistry.