The problem with taking standard batteries is that they aren't very good. Even the lithiums. The reason for this is they are designed as a series of compromises and are limited by the need to be, basically, backwards compatable. That limits your size, and your output levels.

You COULD make a AA-sized battery that puts out MUCH higher current, but no one WILL make it for liability and standardization reasons. It would be fairly easy to develop a CR123 replacement within the AA size envelope, but they won't for the issues I mentioned above. You could make D-sized battery that didn't suck, but no one will for the same reason. That is why your higher perfmance batteries (CR123, CR2, et al) are funny sizes. (Don't ask me why the N and A23, and certain watch batteries, are the same size. Those are the screw ball exceptions.)

When you have a propritary battery back on something that is basically a one use device, it lets you make the battery that is optimal for that device. That means you can get more power for your volume and mass. I've never taken a PLB apart, but you could practically wrap it around the components, reducing waisted bulk.

It also keeps you from thiefing it to power your MP3 player or any such silliness- people do stupid stuff, don't say you'll never do it, because every single person here has put thier back up batteries in a non-esential device, or spent thier emergency $20 on fast food when they didn't have other cash, or pulled some of the bug-in gas off for the lawn mower and didn't replace it right away. We've all done it, it's called being human.