I think the impracticality of using a lipo versus the convenience of regular AA batterie is the reason why many don't.
If you use good quality AA batteries they will last quite sometime and will not pose a hazard if they are accidentally drained.
I use Eneloop rechargeable batteries, they are not the cheapest but they have a phenomenal life expectancy.
I know some people have done this mod, particularly if they want to power other devices off the same battery. But the Phantom's controller lasts for months of flying on a single set of AAs, so it's not a mod of necessity.