what I observed was that the SSD works when plugged in through the USB enclosure but not in the HDD port.
I accidentally figured, if I plugged in a chrome os flex installer USB drive and boot into it while the SSD is plugged-in in the HDD slot. It boots to the Chrome OS Flex welcome page. Now, if you remove the usb drive with chrome os flex, it automatically boots the SSD without any issues. At this point I guess its some issue with the apple boot SW.