Just because something has a theoretical bandwidth limit that is higher than some other theoretical bandwidth limit, doesn't mean that the first will be faster.
As you pointed out, installing an SSD into a USB 3 enclosure will be much closer to the limit of USB 3 than if you install the same SSD into a Thunderbolt enclosure. But again, if the Thunderbolt enclosure -makers don't improve their controllers, there is no real advantage of Thunderbolt in terms of speed.
If they do fix it though, it has the potential to be faster but considering most consumer SSDs are SATA 3 (6Gbps), that speed-advantage is almost nothing. Until more PCIe SSDs come out, having a single SSD in a Thunderbolt enclosure is practically useless in terms of speed-advantage over USB 3.
In terms of other things, CPU-usage, TRIM-support, Thunderbolt do have an advantage. But speed - not so much currently.