- You'd expect the application to run as your user and have full access to the home directory. Many applications expect to have this access. This is what it means to have user space applications. Flatpak is not about fixing or changing this.
- You'd expect individual applications might have out of date dependencies. Depending on the application this might be completely fine. This is not a security risk of flatpak but of the application. Developers are responsible for releasing updates, not flatpak.
So, works as advertised and intended. If your flatpak install has security bugs, update it. If you use a linux distribution that ships an out of date flatpak with fixed security issues, consider using a different one or update it yourself. If you use flatpak apps from developers that can't be bothered to release updates or fix bugs, consider using something else.
Basically, flatpak not being a middlemen between you and the application developers kind of is the whole point. They don't mention sandboxing on their frontpage, at all. This is not a goal. Instead, providing a cross distribution consistent installation experience is the main goal. They are not trying to be more secure than manually installing packages on your system.
So, these are not security bugs as far as I can see. It's not a security nightmare. It's fine. Actually looks interesting and might give it a try if/when I get rid of my mac.