It works the other way round. The factory designed the mounting system brackets of the panniers to fit in a specific position and the toolbox then has to fit round it. If the toolbox is mounted too far back then it has to be moved forward as you cannot move the brackets.For clearance to the panniers, besides the dimension of the tray/lid, it also depends on where the lid is mounted, how far back from the front seat mounts.
Unless you have an oversize non original toolbox then it looks like it's not a problem.