The controller can be any place. Integrated into the chipset, an add-on chip built into the motherbd (try to find out whats its connected to, usually a pcie x1 link), or an addon card like you're looking into.
Ok lets say you put a WD Raptor drive in an external usb3 enclosure and lets say it can transfer data at 150mb/s just for the sake of the example.
if you plug it into the usb2 ports you would see something in the mid 30's to 70mb/s depending on the usb2 controller your plugged in to (some can do 2x speed)
if you plug it into a usb3 pci controller you will see about 128mb/s (133 minus headroom) but anything else on the pci bus needing bandwidth would subtract from that figure. The PCI bus 133mb/s is total bandwidth, not per device.
if you plugged it into a usb3 port on a pcie controller then you would see full speed of the controller up to near the 150mb/s of the harddrives ability. You can only exceed the transfer speed of the drive on small files where it would really be transferring from the drives cache and not the platters.
now exchange that raptor for an SSD at 250mb/s (sata2 speed) and plugged into the pcie USB3 controller and you would see nearly al lof it (250 minus some headroom about 225 I think)
for most external drive, it doesnt matter where the usb3 controller is as platter based HDD's have a difficult time exceeding even PCI bandwidth.