With help from WRC, looks like this is something of our own doing - we were using sub-transforms in ways that caused us problems. Our sub-transforms above were outputting whole new XML documents, when at the very least they should have been taking existing partially produced XML from the top-level transform and using that existing document to output. We "solved" the node ordering issue by moving everything into a single transform, so there was no mismatch between top level and sub-transforms.

For the sake of other people being able to find an answer, we took this up with WRC. Suspicion is this is a bug/aberrant behaviour in Ensemble (and they suspect recent versions of Iris). WRC were going to check in with development, and we are still waiting to hear back from them around that.