I'm not sure what you mean by this. At an effective data rate of 3.2 Gb/s (400 MB/s) after encoding and protocol overhead, USB 3.0 is far faster than any mechanical drive, and will not significantly bottleneck most SSDs.
In practice, I've found SSDs can be significantly bottlenecked, compared to internal or eSATA. That, much like USB 2, different bridges and host controllers perform differently (FI, I have an enclosure that maxes out around 100MBps on a 7-series Intel, but can do nearly 200MBps from an add-on Asmedia chip on an older PC). But, it's worth the convenience, IMO, since the random speeds are still really great, and it can plug into any PC's USB port and work. That 100MBps sequential issue doesn't keep it from doing 50MBps random :twisted:.
For an HDD, though, any significant speed differences are almost assuredly OS caching and buffering settings, and not the USB bridge, nor USB 3.0 itself. Most USB 3 bridges can do 150MBps+, which is plenty to get the most practical performance out of any HDD today.
One advantage for the internal dock option, however, is that you can be guaranteed to be able to boot from, check SMART on, and run diag software on, the HDD, whereas that doesn't always work with USB bridges.