I think the idea here is that, between plentiful Firewire 2 and Thunderbolt 2, you now have enough external bandwidth that you shouldn't need internal cards. When given the choice, I prefer this route, since it means I can transport my proprietary stuff to other machines, or even use them with laptops in a pinch.

That might not work for you, granted, but the amount of bandwidth available between all those ports (20 GB/s in the case of Thunderbolt 2) should be enough to cover most use-cases.