It's just trying to give their devices to a wider market share than a narrow one
My new x99 board has no esata ports it has as yours usb3 and 1 usb3.1

I wouldn't worry about the esata stuff use the new technology as you already are using usb 3.1 as long as the manufacture of the device says there's no problems you're set to go as fast as possible and I doubt adding an esata card is going to improve on that

usb3.1 built into the board without cables except of the devices is likely to be faster same goes for usb3.

If the device has an option for a high speed cable = gold tipped might be as good as it gets ?