In a motherboard with a true eSATA port, does Linux actually distinguish between the eSATA port and the internal SATA ports?

I have a USB hard drive enclosure with both USB2 and eSATA connectors. Since SATA is nominally faster than USB2, I'm thinking if I can get away with installing a cheap mechanical adapter that can extend the internal SATA connector to an ad hoc eSATA port. Or do I need to upgrade to a new motherboard with a built-in eSATA port?

Aside from the physical connectors, are there any other differences, hardware or software-wise, between plain SATA and eSATA?