why does it not matter how long the different fuels had been burning?

You're measuring the total energy yield of the fuel itself (basically the total amount of chemical energy stored in the fuel). To do this, burn the fuel and measure the total amount released.

As you burn all the fuel, and measure all the energy released, the total time this takes doesn't matter. Remember, you're measuring the fuel's energy capacity, not the rate at which it is released.

Of course, if you wanted to, you could also measure how long it takes to burn, and thereby also work out the rate at which it releases energy as well. This would be useful for various purposes, but it would not be telling you kJ/mol