1. the rx480 in its 6pin reference variant uses more power than the PCIe slot is designed for. On a good mainboard that shouldn't be much of a problem, however it's not ideal.
Aftermarket designs will probably connect it with a 6+2pin to the PSU eliminating this issue
2. The reference cooler is a single 75(?)mm fan that exhausts hot air through the card out of the card's panel
While aftermarket designs will probably use 2x90mm fans which will integrate the cooling in the case's solution, keeping the card cooler
3. Given that the reference fan has a lot more to do than the big aftermarket fans and needs high pressure, it will run at high RPM and e of a cheap OEM quality thus making it significantly louder
So choosing an aftermarket twin cooler design will be most definitely be very beneficial