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Programs ran through Flatpak can only access permissions and directories that it has explicit permission for. This is perfect for a very small program that only does one thing, it can get rather awkward when you need it to access multiple storage volumes. For example, I wanted to have my Steam games stored on different hard drives, but they were never visible through Steam. I had to override the Flatpak permission to give access to my mounted disks for it to work.
Programs ran through Flatpak can only access permissions and directories that it has explicit permission for. This is perfect for a very small program that only does one thing, it can get rather awkward when you need it to access multiple storage volumes. For example, I wanted to have my Steam games stored on different hard drives, but they were never visible through Steam. I had to override the Flatpak permission to give access to my mounted disks for it to work.
The fact that we can choose to enhance the permissions beyond their default scope on a case by case basis is powerful.