I'm up and running! That was a right faff...
Ok, short version.
Previously configuring the controller through the PMC MaxView option in UEFI. I suddenly noticed that although I had set the disks to Enabled, they were showing as Disabled. So I set them to Enabled again. Lo and behold, they set back to Disabled. Something was going on with the actual controller config settings.
I downloaded the CLI version of the ARCCONF tool, made a bootable USB, and went in that way. All disks showing completely healthy. I then tried creating a JBOD via the CLI, rebooted, and everything works!! So it would appear that the underlying issue wasn't actually Xpenology at all, but for some reason the UEFI interface not retaining/implementing the settings.
Thank you all for your help, I wouldn't have got through the thought-puzzle without it!