probligo
For our MD80 fleet, the enroute fuel burn is not an issue, even at our max endurance of 5+ hours, since the fuel tanks lie on or near the CG and our procedures require it to be burned so it will not disturb the CG.
On 747s and some other large airplanes (the XB-70 and Concorde, before it stopped flying), fuel is stored at locations far away from the CG ( in the horizontal stabilizer for long distance flights on the 747-400, for instance), so flight crew procedures are developed to ensure the fuel is burned so as to keep the CG in limits.
As I recall, the Concorde and XB-70 also moved fuel to retain the optimum CG as a function of Mach number, but that is the extreme limit of my understanding....
HTH
Jim