In practise, Flatpak packages have many more permissions than you might expect, and the sandbox feature gives a false sense of security. For example, the Obsidian Flatpak package [0] is given all of the following abilities without explicit permission from the user (the user has to know where to look to find out about them):
- Home folder read/write access
- System folder media
- System folder mnt
- Microphone access and audio playback
- And more...
The Obsidian snap [1] is installed with the --classic flag, which also grants access to the whole home directory, but at least you have to consciously specify the --classic flag to grant this permission.
[0] - https://flathub.org/en/apps/md.obsidian.Obsidian
[1] - https://snapcraft.io/obsidian