Well I ended up re-installing OMV. Not just because of this issue - I've been running the OS from an SD card and I came into possession of an eMMC (and couldn't just copy the image from one to the other - don't ask).
Anyhoo, on first boot up, everything ran fine, with no pausing or Ctrl-D'ing necessary. Just booted right on up. The hard drives were recognised as a raid configuration, although the raid (/dev/md127) wasn't mounted. Did a bunch of configuration. When I went to reboot - guess what? Yup, had to attach a keyboard and Ctrl-D.
In syslog there was a message about the mountpoint again, but I'm not convinced this is where it's pausing for the keyboard input. The message was right at the end of syslog. But I've run out of time to mess around with this. I'm resigned to having to attach a keyboard and hitting Ctrl-D, then going in via the web interface and mounting the raid. Selah.