In most cases, Flatpak is not more secure than anyone’s normal packaging format, as:
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Flatpak app permissions are set by app developers without any interaction from the users when using the apps, i.e. there’s no prompt for those permissions to the users, contrary to PWAs, for example, where app permissions are set but needed to be allowed by the users first.
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Many Flatpak apps are packaged by community. If security is concerned, there’s no alternative to official packages.