Are the taxa sorted based on their percent abundance (from largest to smallest? I initially thought this was the case, but it seemed that it was not? Or perhaps I made some mistakes?
Looking at the example visualization from QIIME 2 View, and also some of my own QZV files, I think they are ordered based on overall abundance across all samples/conditions... I'll search for any hint in the plugin code and update this comment with whatever I find.
Edit: I could not find any explicit ordering in the code, but some issues in the GitHub repo (#5, #25) imply that the order is based on abundance.