Where you run a random script from some random guy who is likely unassociated with the project which has very little chance of being audited?

Until recently, most Flatpaks were also published by random people and you had no easy way of verifying who they were.

In that case, yes, one could have a poorly sandboxes app, but the vast majority have some to a larger amount of sandboxing

That is not a usable argument for security. The app developer sets how much sandboxing their app gets, so if they want your data, they can get it.

And sure, you can restrict permissions yourself if you want, but that’s not what any normal user does.