The idea for adding space for the tool in question came about by accident, and during the course of using my tools and then having to pack them up and move them. I happened to set down the tool on the toolbox in a place shaped like the tool, and I looked at how much space it appeared to have in the hollow cavity. After I put the tool against the box and checked it in a few directions I felt sure enough that I would have room that I decided to go ahead and cut into the toolbox.
Again, you have to be careful and make a judgement call on how much material you can remove and not affect the structure of the box, as well as have unintended consequences as far as removing tool support profiles in the molding portions. In this case, there were two tools in the area I wanted to remove, so I took a close look at how those tools would be supported and held in place if I cut out the area large enough to get a new tool in place. The main concern in my toolbox was the reciprocating saw, but it was supported on several surfaces so removing what I needed to would not affect the support.