Performance should be exactly the same if you're comparing a Promise card to an on-board Promise controller, as they both would be the same chipset and both pass over the PCI bus. Same would apply to cards and boards with other chipsets. Obviously you can't compare an onboard Promise chipset with a Highpoint card.
Thinking about it though, there might be very slight differences in the design such that the onboard controller would not be perfectly optimized as the Promise card would be (sort of like a Crucial memory module is expected to be better than other brand modules that use Micron chips). The motherboard maker has to design the board layout so that the chipset connects to the IDE ports and then has to connect to the PCI bus. Promise making their own card, they're able to optimize it since they only have to worry about connecting the ports to their chip and then into the PCI slot. I don't think it'd make that huge a difference though.
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