I'm not saying that the feature doesn't make sense.
I'm saying that it doesn't make sense that these settings can be edited more than one place and that one of the places is the global Components, Install Packages dialog.
After all if I still get confused about this after using Delphi for 24 years, then there's either something wrong with the UI or I'm just slow.
Change the global dialog so it doesn't edit the project package list and instead make it clear that it's editing the default options and there's no confusion.
Even better, and I remember this was discussed ad nauseam some twenty years ago, but if the package list had been opt-in instead of opt-out then much of these package juggling problems wouldn't exist.