Alas, right now it is all flat.
But, I do see the need to move on up to having
broader-than/narrower-than relationships. For that step, I'd like to see
it move to an SKOS-based system, but that's a step I probably won't be
able to get to in the near future.
A shorter-term solution might be to add a ControlledVocab_BroaderThan
table to the plugin to handle that kind of data. I'll spend some time
mulling over the options for how that might work.
Sorry it looks like it won't fit what you need right now, but the
question tells me good stuff about more use-cases.