The best way to approach the issue is to choose the best possible motherboard.
If you can get that unit with TI chipset Firewire, go for it.
If not, add a quality TI chipset FW controller.
Real-world, it doesn't matter whether you use PCIe, PCI, or onboard.
Assuming quality units, you'll achieve the same results either way...
IOW: Going with PCIe (or onboard) will not allow you to achieve lower latency.
As to whether a Via Firewire controller will work well...
Totally depends on which Via controller... and the audio interface it's paired with.
Go TI... and you've tremendously reduced the odds of having a problem.
Almost every time you see somone having issues with a Firewire audio interface, they're not using a TI chipset controller.