The issue with using powered risers would be drawing more than 75w thru them since the 6 pin pci-e is insufficient to supply all the power the rx 480 needs it will try and draw any additional power thru the powered riser which is likely to result in melted molex connections.
This is the reason I don't use the molex to sata pigtails that are usually supplied. Mine are soldered directly to the holes on the riser board, although you should have no problem using the molex connectors from a good PSU. Molex connectors are supposed to be rated at 11A per pin which means a 12v molex connector could supply 132 watts per card.
Connecting directly to the motherboard means the circuit board traces and ATX pins have to supply 3 cards not just 1.