eSATA is SATA, just with a different connector. There is no other difference.

Except.. with multiple drives sharing a single (e)SATA port, they obviously have to share the 6gb/sec bandwidth of the single port. With Thunderbolt, much more bandwidth is available for port-expanders which might be designed to use it.

And some motherboard SATA controllers are wired with port-multipliers in mind, whereas others omit the extra logic needed to share a single port with multiple drives.

I think I gave a link to one or two Thunderbolt native drive enclosures earlier too, I haven't used any of these though, and to even consider one it would have to have an alternate interface of some kind (eg. regular USB3) to enable drive access from non-thunderbolt systems -- I wouldn't want to be stuck unable to retrieve files when the primary system is kaput!