An integrated charging circuit in the flashlight is more versatile for sure, but the main benefit of USB chargeable flash (for me) is the ability to charge without taking out batteries, not the ability charge with any USB port anywhere. (with the integrated charging circuit you still need to bring the USB cable, right? 
)
Also a separate charging adaptor with be higher quality than a tiny charging circuit in the flashlight. And i really i like the idea of an magnetic connection.
A problem is the risk of short circuit the battery, but i think (not sure) a simple diode or something similar can prevent that