Good question. It must take a lot to power up the internal drives so it has to happen during bootup. But having a Raid controller is new to me, so I couldn't tell you. I think an external enclosure can be turned off and on at will because it's self-powered. Hope you find the answer.
ARe you happy with the Raid controller otherwise? My Write speeds are phenomenal, but Read speeds are much slower-about half. I need some time to troubleshoot.