It does help greatly in general though, because all of your data will be encrypted when the device is at rest. Theft and B&Es will no longer present a risk to your privacy.
Per-app permissions address this specific threat model directly. Containerized apps, such as those provided by Flatpak can ensure that apps remain sandboxed and unable to access data without explicit authorization.
Full disk encryption doesn’t help with this threat model at all. A rogue program running on the same machine can still access all the files.
It does help greatly in general though, because all of your data will be encrypted when the device is at rest. Theft and B&Es will no longer present a risk to your privacy.
Per-app permissions address this specific threat model directly. Containerized apps, such as those provided by Flatpak can ensure that apps remain sandboxed and unable to access data without explicit authorization.