So I finally read the release notes for Unraid 6.12 as I was preparing to update my server today. Turns out they DID address the FUSE issue. Or rather, they gave us a built-in way to bypass FUSE in the correct circumstances. For the curious, read the “Share Storage Conceptual Change” section of the 6.12.0 release notes.
Honestly, that’s good enough for me to consider this issue resolved.
After upgrading Unraid, I did set up my appdata share to be an “Exclusive Share,” which is the signifier in Unraid to bypass FUSE. I updated my Duplicati config to undo the previous workaround to bypass FUSE manually. I will report back if I experience slowness again, but I expect it will work well.