I'm with you Tarquin. See my other message (some reason it has not turned up in https://www.mail-archive.com/therion@speleo.sk/) Seems like it is intentional, but it is more complicated than that. This page describes https://therion.speleo.sk/wiki/contrib:externalviewers#examples_of_rendering _differences_between_pdf_viewers
I had not realised that this would cause me issues! FWIW, I would prefer that rocks do not obscure a passage stacked below their scrap completely. I do not mind seeing water as translucent below a rock when the rock sits in the water. I very much like the look of boulders as a translucent overlay on top of water, since we have situations where boulders sit in water, and that was a great way to represent them as a boulder with water underneath. You could then use "placement bottom" to put a boulder underwater, such as a shallow area within a lake. Either way, you could see a second passage hidden underneath the first. I do not care much for Adobe Reader and its inability to draw layered opacity (which has caused issues for other applications that create PDFs such as PrinceXML). It's an awful PDF reader. Foxit, Sumatra, Evince; these look great to me, and the others the who were discussing the output with me today.
I had always thought double rendered translucent objects where the intention, but seems they are not. I would vote for making it an option (not withstanding what you actually see will depend on the viewer used).
+9 If someone uses Adobe, they get junk. So be it. Let good PDF viewers display it nicely please. :)