I wish to add some user feedback here. I am not sure how I could be confused by the fact that option that I set is persistent. At the same time, checkboxes that are reset every time you see them are common in UI concept known as "wizard". So if this is considered as something that you should consciously tweak every time than it could be a popup shown when user make changes to packages (similar to how conflicts are interactively solved). Personally, I would prefer these options where they are now as it does not look as if I will change them frequently.