USB devices _do_ incur extra latency. The USB apollos do suffer from this. The firewire and thunderbolt do not.
Whether a devices is internal or external is irrelevant. There are "Internal" devices that are PCI based which have excellent performance, and external devices that are Thunderbolt based with equal (and better!) performance characteristics.
I believe you're talking about onboard sound, not "internal", in which case you're correct. However, that's not what the link is talking about.