I think the difference in fuel usage is down to the software used, not a 100% sure.


In 2002, for purposes of increasing safety, regulation changes related to weight, available fuel and engine capacity were introduced. Reducing the amount of available fuel over race distance requires an engine to run more efficiently, thereby reigning in power. A regulation allowing maximum of 26 litres was introduced in 2004, with that number incrementally lowering throughout the decade. Fuel tank capacity was reduced to 24 litres in 2005, and reduced a further 2 litres to 22 in 2006. From 2007 onwards the FIM regulated that engines were limited a maximum fuel capacity of 21 litres in MotoGP class, with 2014 seeing a further drop to 20 litres. The so-called “Open class” may run up to 24 litres.
Races vary in length from circuit to circuit, and the demands of a certain track may mean that it results in higher fuel consumption for the bikes than other tracks of similar length. Teams can measure how much fuel they are using during qualifying and free practice sessions to ensure that just the right amount is in the tank when the race starts – as of course carrying unnecessary fuel could mean the fraction of a second which loses a race.
In qualifying, the fastest times are often set right at the end of the session when the rider is fully warmed-up, his tyres are giving him maximum grip and - having emptied most of the tank - a lighter fuel load allows him to lap as quick as possible.
Fuel is specially produced by the various fuel companies and is very precisely adapted for racing. The final product is only slightly different to the sort of fuel used by the general public, but must be approved for use by the FIM.
The components are 99% the same as road fuel, but suppliers can alter the levels the hundreds of various components which fuel comprises to ensure they are using exactly the right blend of anti-oxidants, detergents, friction modifiers and so on to improve efficiency.
LUBRICANT
In addition to fuel, lubricant suppliers provide the teams with race modified engine oil, to lubricate and therefore reduce friction, which produces better fuel economy. This in turn means the bike can carry a minimum amount of fuel.
MotoGP lubricants are based on a standard product, as is the fuel, though the racing product varies more with lubricants than with fuel. The oil has to lubricate the engine’s rotating parts, the gearbox’s constantly moving components and of course the clutch itself, which inevitably all get extremely hot on track. The more efficient the lubricant is the less fuel consumed and the better the bike performs, giving its rider a greater chance of victory.
From 2014, teams not directly entered by one of the major manufacturers as a factory team or satellite outfit, will be categorised in the so-called “Open class”. Whilst all factory teams (MSMA entries) will have to use the spec Magneti Marelli hardware with their own software, the “Open class”, regardless of its mechanical make-up, will run the spec hardware as well as software. From a mechanical standpoint, the “Open class” in 2014 will consists of full-blown prototypes (with Magneti Marelli software), prototype chassis with factory-spec engines, as well as heavily tuned production engines in prototype chassis.