For FC, SAS and Ethernet onboard I haven't noticed a difference between those and PCIe cards. I some cases the onboard may be the same ASIC too but not always. For 10gb onboard the Sfp+ may be a different model but I haven't seen any performance numbers showing a difference although there might be a slight difference I haven't noticed. But hasn't been a concern using the same onboard or pci for the same speed port.
For Ethernet and Ifgrps (lacp for example) the network admin guide best practice is to use the same card type with the same ASIC. So best to create lacp on different cards of the same model. Makes sense since there was an old flow control bug and also the same exact ASIC performance on the same card model.