I must admit that I did make a rookie mistake, and somehow ended up keeping ACMT-merged descriptions active when I thought that my add-on.xml file was supplying my custom trees. But as has been pointed out here, it doesn't work that way. I had hoped that I could get away without making a single change/addition to the Prepar3d installation folders, but it isn't as simple as I thought.
The ideal solution might be to use ACMT to merge my descriptions with the default, but save them in my add-on folder. On the other hand, one of the reasons why I like and use ACMT is that other developers change the default files anyway, so I'll probably just carry on as usual, installing ACMT with my scenery, and running it as I've done with FSX and P3Dv3. The only problem here is that I can't add my scenery using add-on.xml, as ACMT doesn't pick it up when it runs.
So it's back to the drawing board, installing scenery using the command-line method. Has anyone come up with a better solution?
At the moment, I have a merged descriptions file in a folder pointed to by add-on.xml, I just need a way to get it there for my users.