For some keyboards, it makes a difference. From what (little) I know about capacitive matricies, the way IBM did their matrix is easier than a 12*12, what with all the sense / scan lines. For most regular keyboards I imagine it can't make too much of a difference, but it's probably easier to program the way they did it.
Another option is that it'd be much easier to lay out the traces that way. With a matrix that's different than your key configuration, it would start to get very difficult indeed to get it working on your PCB. In the olden days, you didn't have a computer to route your PCB lines, and in the modern era, the PCB is often one-sided. In both cases, you only have so much room for your traces (unless you use super thin traces like vortex)
Zustiur, I think that might be called the nav cluster, but I'm not sure on that.