Presumably its only opt-in to the application you want to use it with. If this new system was applied to all applications by default, yeah it could become a problem. The reason why the permission control in Android and Flatpak works is, because those applications and packages are designed and built with these limitations by default and the user should not need to modify the permissions. There are a few cases (in Flatpak) where you need to change the permission, which is annoying, especially if you don’t know. How worse will it be with applications that are not designed with these limitations in mind and force them with permissions taken away with this new tool?
Overall I don’t think it’s such a bad idea to have a technology on your hand to limit permissions and access, but it needs to be opt-in. In example this could be useful for AppImages, that are downloaded from the web and not managed by your operating system or a community like Flathub.
I call this quite a… “commitment” to version 0.1.0.