Flatpak has a sandbox; but for some apps, it has to be a more open, otherwise they would not work as intended. All that's open is visible as a flatpak permission; if you want, you can tighten it up and see, what breaks.

On the other side spectrum are people, that are disappointed, that they cannot use SDKs installed at random places in their host system with editors packaged with Flatpak. Well, duh...