I was told once that, for USB connected drives, you need sdparm instead of hdparm. I was drawn away to other issues before I ever tried that so I don't know if that will help.
Sdparm works with SCSI-disks, and sometimes works with USB-drives, too. I don't know what is exactly standard busybox command set (probably there is not any...), but this piCore busybox has just hdparm. Problem is more RAID function than USB, if different type disks are allowed, is impossible to make setup transparent for both disks.
Hdparm is typically used to set DMA-transfer parameters and sleep timing, and if those are set directly by IDE (this case sata) connector, there should not be problems. Of course, if application try to set those parameters and error returns, there is a problem.
I do not see any reason for Cherokee to set those parameters.