The problem: It can be either cooperating with other users with another version of ArcGIS Pro or yourself realising after saving, that the newest version of ArcGIS Pro does not work for you. ArcGIS Pro should then also the next times that you click on save, stick to the chosen version, including the gdb, tbx etc..
I do not work with toolboxes or geodatabases, so I want to avoid the hustle of clicking through the packaging process, only the to remove the packed data and restore all old paths. And for cooperating with other people, you might want to have the option that everybody can make changes and simply save, especially because it is the superuser who often updates the license quicker, and would after every change need to package the project again.
I could imagine that this suggestion has already been made, but I cannot find it.