I do not know what 'recent' PCIe board update from Inatek you are referring to. As far as I can see their current card is still the KT4004 which their own website specifically states is not compatible with Yosemite or El Capitan.
See - http://www.inateck.com/pci-e-to-usb-3-0-cards/inateck-kt4004-4-port-usb-3-0-pci- e-express-card-without-power-connection.…
Many users have reported it working well enough in El Capitan although I seem to remember seeing a couple of reports suggesting which PCIe slot you use may have an impact. The issue regarding USB drives disconnecting when you wake your Mac is a wide-spread issue that also affects many people even when using the built-in USB ports.
The only two brands/models I am aware of that categorically claim El Capitan compatibility are SonnetTech and CalDigit.
See -
http://www.sonnettech.com/product/allegrousb3pcie4port.html
http://www.sonnettech.com/product/allegroprousb3pcie.html
and
http://www.caldigit.com/FASTA%2D6GU3plus/ (Also does USB3.1)
Note: The two SonnetTech cards do not need a cable for internal power, and can actually provide enough power to fast charge iOS devices, I therefore think they should be fine for hard disks. As a reminder only 2.5" hard disks can run off USB power, a 3.5" drive in a USB enclosure always needs an external power supply.