Chris, sorry again you’re sort of stuck in the middle of the two companies with this particular issue.
Since others stated it’ll be fixed in an upcoming release (including Woo’s support), we’re going to go with that for now.
Once their update is officially released, you’re welcome to bring this topic up again. We, of course, don’t want issues between our two plugins, but our plugin simply registers the custom taxonomy and FUE does things from there.
Again, if they have specific code recommendations for us, we’re more than happy to address those.