the cables are the same. the only time a cable that fits won't charge a phone is if the phone looks for an IC that allows it to charge (older moto phones were notorious for doing this)
this was one of the reasons companies went from proprietary connections to mini and then micro usb.
i do agree that an extremely long cable can cause data loss, but for charging, if it does ANYTHING, it'll charge slower.
in all likelihood moto gave us a usb brick and a separate cable because it means they only have to give us one cable instead of a power adapter with integrated cable and then a separate data cable.
fwiw, i've used the cable that comes with the phone, a generic micro cable i bought, my friend's tour cable, a storm cable, and the generic verizon car charger. they all worked just fine.