Sorting with the button sorts and correctly updates the items visually, but middle-click sorting (which I got into the habit of doing from InventoryTweaks years ago) only sorts the items "internally", with no visual change.

I'm not sure how this can happen since both methods just call sendSortPacket but it somehow does.

Do you have middle click bound to anything else?

Pick Block, by default. I cloned the repo and the same thing happens in the dev env, no other mods.

If you unbind that does the issue persist?

Yes the issue goes away when pick block is unbound.