Ideally, we get the best of both worlds. The isolation technology that Flatpak uses (bubblewrap) isn't exclusive to Flatpaked apps, so someone could probably make a distro with isolation by-default if they were motivated enough.

> What distro would you recommend to somebody like me who wants to be asked before an application gets access

Use an immutable distro like Silverblue or Kinoite. Those are more-or-less Flatpak-only, extremely stable and fairly rigid with security.