For future reference:
I posted this question a while ago and I’ve found a work-around since. Though I would still class this as a bug.
To fix this I reworked my landscape layers so that all painting was done on one layer. It seems the trace only detects surface types on the base layer.
I also switched my workflow to work exclusively with weight blended layers. It seems having non-weighted blends is not compatible with this approach either. I find this a bit tricky with my painting workflows though especially with using the paint erasing tools.
I’ll need to come up with a workflow that results in all my paints being on that single base layer…