The performances are the same, usually, the only difference is the possibility to modify some controller option (particularly the stripesize) with the PCI card.
Moreover the onboard raid controller should use the drivers released by the motherboard manufacturer, while the PCI RAID card can use the drivers supplied by the RAID controller manufacturer.
______________________ <font color=red>A straight line never ends……………….until it comes up against a vicious circle</font color=red>