Based on the photos in the Icydock link, it appears there is no controller interface in the unit. It appears it draws power for all three HDD's from 2 4-pin Molex connectors from the PSU, and the data connections for the three HDD's are each individual connections directly to a mobo SATA port, so the mobo's controllers are the only ones involved. Even the unit's eSATA and USB ports on the front panel have separate cable connections back to mobo ports.
OP, to settle whether or not the Icydock system somehow is causing this long process, can you connect one of your new drives just directly to a mobo port and power connection, and try it that way? By the way, I assume you have used some method of Partitioning using GPT, not MBR, right?