"do not automatically update" flag
Apps which have new permissions will not be updated automatically nomatter how your flags are set. Additionally, pressing "Update All" does not update those apps - it notifies you of changes* and prompts you to accept or skip the update. I have a number of apps in my Updates list which have been there for many months following the introduction of an unnecessary invasive requirement.
It *used* to notify you of the changes, but after their "simplification" of the permissions system it just says that something is different and leaves you to work out what it is.