Hi,
Thank you for the details, it helps us a lot!
That is because the index table is used only for Post Type content – Users and Taxonomy Terms are fairly nicely indexed by core WordPress.
I can however take this as a feature request to make a separate index for the users as well in a future release. It should not be too complicated to implement, as the code could be shared to some extent with the current index.
We have a few major updates coming soon, so this may not happen in the nearest future, but this is up on the future features list now.