because the package build script isn’t available?

What are you talking about? Every Flatpak on Flathub has their build manifest available on GitHub, you can fork or download it for yourself and change it how you'd like, just like you can with an Arch PKGBUILD

And the problem still isn’t solved because now the people who can set bad defaults still exist, they’re just different people.

For one, unlike with distro packages, lots of Flatpaks are made by the developers of their apps, so bad defaults aren't really going to be a thing for those since the developer would want to choose what's best for their own app

And for packages maintained by a third party, bad defaults are less common because maintainers don't need to account for each individual distro's unique package situation or specific dependency versions, and only have to package it once for every distro

Aside from all the things Flatpaks get right, a sandbox framework built right into the design is a major win and in my case, it's one of the big reasons I went with it.

You can also modify the build script for any flatpak's manifest and create packages with flatpak-builder. May not be as easy as PKGBUILDs but it's certainly possible.

The problem of bad software defaults is easily solved with Flatseal. My point is that, it takes a few clicks to deny permissions to Flatpak applications as opposed to sandboxing a traditional app yourself.

Writing sandbox profiles for apparmor or something similar is usually a complex elaborate affair. And even when you do finally manage to get a working profile, it still requires maintenance to keep the sandbox functional as the target software updates. You won't face any of these problems with Flatpak's bubblewrap.

I can't find that flatpaks are mentioned in that article

I guess mostly sandboxing, permission control, distribution and reproducibility