Right, I managed to work out what was going on here.
I think the harness connection to the pull-down motor disconnected whilst it was in action. This left it "jammed" in position. The main latch (which the keyblade controls) was open, and the car was happy that it was open - hence the warning message.
Thanks to various searches I worked out how to remove the boot lid trim (easy), find the pull-down motor (harder, but using part searches to see what it looked like helped) and then use an allen key (I lent mine out so only had imperial to hand, a 7/32" one fit, using trial and error) and manually rotated the motor.
Then to test it, I hit the "boot open" button from my location lying in the boot with dropped rear seats, and because I hadn't disconnected the trim and the interior lights, when the boot surprisingly raised everything got pulled out of the car and onto the ground, with the trim dangling from a few small wires. I felt pretty stupid about that.
Still 100% buzzing from sorting it out. Will possibly need a new pull down motor, but will check the harness first.
Thanks again for your response, it spurred me into continuing to try stuff.