Just looking at the weird scaremongering around Signal from the past few days ("a chat app stores keys as files that you can read) shows a trend that I’ve been seeing more the past years: people have gotten so used to the Android/iOS sandboxing system that they’ve either never been taught or have forgotten how normal programs work.
Flatpak and the necessary desktop portals are very much a work in progress when it comes to user friendliness, but they’re what the world has been moving towards for a while now.
I don’t know why a journaling app needs full system access and access to system settings, and the permission Flatseal requests is a dangerous one if you pay attention to these things. Looks like they’re doing their job to me.