Hi, a quick update on this - my main startup drive failed a few weeks ago (it was 6 years old so not unexpected), and it just so happened that my most recent full backup made with SuperDuper was to the LaCie USB 3.0 drive that wouldn't boot, described at the top of this thread.
So - I got the startup disk in my iMac replaced, and used SuperDuper to do a full restore from the LaCie USB 3.0 drive.
I'm happy to report that I could boot absolutely normally from the restored image on the new startup disk - even though the drive I restored it from wouldn't boot over the USB 2.0 -> 3.0 link.
There were a few
minor oddities, but I don't think they were in any way related to the USB 3.0 / booting issue - hence I've described these in a separate thread.