Hi! I think a lot of it depends on what you're planning on doing with the data later on. Are you going to train a model and if so, what are you going to predict? This also decides whether there's something you can automate, or whether you can restructure the task to make it easier and faster to annotate.
I agree that framing it as a dependencies/relations task is probably overkill here because you're not actually annotating relationships between words in a text, right? If you already know the structured taxonomy, it probably makes sense to also present it this way. One option would be to just add a simple custom HTML UI with some checkboxes – see here for an example: Asking multiple questions in one task (different input types)