OK, fingers crossed it is fixed now. I'm pretty sure the water wasn't coming from the washer tube, as it did on my earlier Octavia. The pipe junction is more substantial than the earlier one and there was no sign of leakage. However, the big rubber vent mentioned above was loose in its fitting, and when I looked more carefully today I saw that there are two clips on each side of the unit which were not engaged. You can see the nearer two in the photo above. I clipped them all in place and immediately noticed residual water squeezing out of the foam rubber seal on the back of the vent...
There are several videos on YouTube about the Golf problem @pikpilot mentioned, and it seems as though on the Golf the water originates in the roof gutters and gets to the vent via the back lights. I don't think that can happen on the Octavia. However, I remember a few weeks ago hitting a puddle in the Lake District a bit faster than I intended, and it turned out to be a bit deeper than I thought. On the Octavia the boot vent opens into a void between the inner and outer bodywork just behind the wheelarch, and without taking the exhaust box off to have a look, it appears likely that water could get jetted into there in those circumstances.
So, boot and spare wheel well dry, brake light working correctly, all the internal panelling back in place (finally). I'll report back if it turns out not to have worked. Thanks for your help, @pikpilot.