SkyRP,
If I'm reading your query right, my explanation is as follows.
Given that the Main tank transfer pump/s deliver fuel to the supply tanks at a rate greater than both engines at maximum power can suck it from both the supply tanks, the manufacturer believes and teaches that at the point where fuel transfer from the main tank ceases, the supply tanks will be full. From that starting point with engines sucking very similar flow rates from their respective supply tanks, the warnings will occur at different times, and the engines will flame out at different times. The supply tanks have the same manufactured capacity with the exception that one of them has a foam core inserted to take up the space that would otherwise be occuppied by fuel (4kg ish). It is my experience that this sequencial warning is what happens rather than simultaniously.
Just to summarise, the supply tanks should never have the same amount of fuel.