Hello. With eSata also on my Caldigit USB 3.0 card, I am able to boot from an external HD. With the ext HD connected to the USB 3 port no go. There is this thread about problems in booting using USB 3.0 with a Retina MacBook Pro with USB 3.0 ports. They also could not boot when the external HD is connected to the USB 3 port of the rMacbook Pro. But with USB 2.0 they are ble to boot.
https://discussions.apple.com/message/23362502#23362502
At first I thought the USB 3 has to be embedded to the logic board to make booting work. Though not exactly perfect, satisfied with Caldigit USB 3-eSata combo