This certainly appears to prevent the error but, testing with a non-array drive, either the drive does not spin down, or it spins up again very quickly.
I will try moving an array drive back onto the LSI controller.
EDIT:
Okay, I moved one of my array drives back onto the LSI controller and started up. I clicked the 'spin down' button and all the drives appeared to be spun down, but there was a repetitive clicking coming from the server. On inspecting the syslog there was an "mdcmd spindown" for the drive on the LSI controller every eleven seconds.
Jul 22 07:47:02 Tower emhttp: Spinning down all drives...
Jul 22 07:47:02 Tower kernel: mdcmd (28): spindown 0
Jul 22 07:47:03 Tower kernel: mdcmd (29): spindown 1
Jul 22 07:47:03 Tower kernel: mdcmd (30): spindown 2
Jul 22 07:47:04 Tower kernel: mdcmd (31): spindown 3
Jul 22 07:47:05 Tower kernel: mdcmd (32): spindown 4
Jul 22 07:47:07 Tower emhttp: shcmd (61): /usr/sbin/hdparm -y /dev/sdb &> /dev/null
Jul 22 07:47:10 Tower kernel: mdcmd (33): spindown 2
Jul 22 07:47:12 Tower kernel: mdcmd (34): spindown 2
Jul 22 07:47:21 Tower kernel: mdcmd (35): spindown 2
Jul 22 07:47:31 Tower kernel: mdcmd (36): spindown 2
Jul 22 07:47:48 Tower kernel: mdcmd (37): spindown 2
Jul 22 07:48:11 Tower emhttp: Spinning down all drives...
Jul 22 07:48:11 Tower kernel: mdcmd (38): spindown 0
Jul 22 07:48:12 Tower kernel: mdcmd (39): spindown 1
Jul 22 07:48:12 Tower kernel: mdcmd (40): spindown 2
Jul 22 07:48:13 Tower kernel: mdcmd (41): spindown 3
Jul 22 07:48:14 Tower kernel: mdcmd (42): spindown 4
Jul 22 07:48:16 Tower emhttp: shcmd (62): /usr/sbin/hdparm -y /dev/sdb &> /dev/null
Jul 22 07:48:17 Tower kernel: mdcmd (43): spindown 2
Jul 22 07:48:19 Tower kernel: mdcmd (44): spindown 2
Jul 22 07:48:31 Tower kernel: mdcmd (45): spindown 2
Jul 22 07:48:33 Tower kernel: mdcmd (46): spindown 2
Jul 22 07:48:43 Tower kernel: mdcmd (47): spindown 2
Jul 22 07:48:45 Tower kernel: mdcmd (48): spindown 2
Jul 22 07:51:26 Tower emhttp: Spinning down all drives...
Jul 22 07:51:26 Tower kernel: mdcmd (49): spindown 0
Jul 22 07:51:26 Tower kernel: mdcmd (50): spindown 1
Jul 22 07:51:26 Tower kernel: mdcmd (51): spindown 2
Jul 22 07:51:27 Tower kernel: mdcmd (52): spindown 3
Jul 22 07:51:28 Tower kernel: mdcmd (53): spindown 4
Jul 22 07:51:30 Tower emhttp: shcmd (63): /usr/sbin/hdparm -y /dev/sdb &> /dev/null
Jul 22 07:51:31 Tower kernel: mdcmd (54): spindown 2
Jul 22 07:51:34 Tower kernel: mdcmd (55): spindown 2
Jul 22 07:51:39 Tower kernel: mdcmd (56): spindown 2
Jul 22 07:51:45 Tower kernel: mdcmd (57): spindown 2
Jul 22 07:51:48 Tower kernel: mdcmd (58): spindown 2
Jul 22 07:51:56 Tower kernel: mdcmd (59): spindown 2
Jul 22 07:52:07 Tower kernel: mdcmd (60): spindown 2
Jul 22 07:52:18 Tower kernel: mdcmd (61): spindown 2
Jul 22 07:52:29 Tower kernel: mdcmd (62): spindown 2
Jul 22 07:52:40 Tower kernel: mdcmd (63): spindown 2
Jul 22 07:52:51 Tower kernel: mdcmd (64): spindown 2
Jul 22 07:53:02 Tower kernel: mdcmd (65): spindown 2
Jul 22 07:53:13 Tower kernel: mdcmd (66): spindown 2
Jul 22 07:53:24 Tower kernel: mdcmd (67): spindown 2
Jul 22 07:53:35 Tower kernel: mdcmd (68): spindown 2
Jul 22 07:53:46 Tower kernel: mdcmd (69): spindown 2
Jul 22 07:53:57 Tower kernel: mdcmd (70): spindown 2
Jul 22 07:54:08 Tower kernel: mdcmd (71): spindown 2
Jul 22 07:54:12 Tower mountd[3993]: authenticated mount request from 10.2.1.15:936 for /mnt/user/Movies (/mnt/user/Movies)
Jul 22 07:54:12 Tower mountd[3993]: authenticated mount request from 10.2.1.15:994 for /mnt/disk1 (/mnt/disk1)
Jul 22 07:54:19 Tower kernel: mdcmd (72): spindown 2
Jul 22 07:54:19 Tower mountd[3993]: authenticated mount request from 10.2.1.15:994 for /mnt/disk1 (/mnt/disk1)
Jul 22 07:54:30 Tower kernel: mdcmd (73): spindown 2
Jul 22 07:54:37 Tower login[3499]: ROOT LOGIN on '/dev/tty1'
Jul 22 07:54:41 Tower kernel: mdcmd (74): spindown 2
Jul 22 07:54:44 Tower shutdown[9032]: shutting down for system reboot
Jul 22 07:55:10 Tower init: Switching to runlevel: 6
Jul 22 07:55:18 Tower rc.unRAID[9331]: Stopping unRAID.
I quickly reverted to my previous configuration.
It is clear that, with the line added in the go script, the original errors go away - whether this is because the spindown never happens, or the fault is really circumvented, I'm not sure. However, I was not happy with the repeated clicking and 11 second spindown commands.
Also, during my testing, I had a lock up of all user interfaces - emhttp and unRAID both became unresponsive, the system console wouldn't produce a prompt and I couldn't get a telnet connection.
Whether anything is learned from my testing, I'm not sure, but this is definitely NOT a solution!