At worst the "joke" sandbox value of flatpaks is the same as deb/rpm packages and snap "clasic" confinement. So as a user, you don't lose anything security wise by moving to flatpaks.

Flatpak, as well as snaps through clasic confinement, allows the developers to "escape" the sandbox because they know that they don't have all the permissions required to provide feature parity with deb/rpm packages. Another reason this is needed is that application developers are not writing their applications with flatpak compatibility in mind. However flatpak is going in the right direction.

Mobile operating systems have proven the value of sandboxing apps.