Sorry for the delay in getting to this issue. I agree that this is frustrating. Can you help me think through a better way to do this?
Here is the issue as I see it. I offer a manual and automatic mode for the sort. The idea is that if you are not a developer or don't want to do anything order than turn on the plugin and have it sort by the custom order, you run the plugin in automatic mode. If you do so, EVERY place that the terms are displayed will be sorted according to the custom sort order. The alternative to this is the manual sort mode where you can control the sort order by placing an argument in the call to get_terms. The custom sort will then only be applied in cases where the get_terms arguments have been properly modified. In manual mode, the sort order on the taxonomy page will not be affected.
Would the correct solution in your opinion be to override the sort, regardless of mode on the taxonomy page? Does that seem logical?
Thanks for the input and helping me provide a better experience.