The license of the boxed version allows me to install Aperture on one desktop machine and one notebook computer. The AppStore license allows me to install and use the software on all "personal" computers. And the last time that I looked, all of my machines were "personal" machines.
Okay, this probably makes a difference for business users where several people use the same computer. But as we all know, you hardly find Macs in businesses, so probably nobody will ever notice that difference in the licensing terms...