>As we also open the ability for applications to be uploaded in binary form, which is essential for low-friction compatibility with popular language-specific build systems such as Electron/Node, Rust, Go, etc - we also reduce the ability for users to scrutinise the source in the Flathub build system that was used to build their application.
This is unacceptable. Open-source apps should always be built from source on a trusted infrastructure and ideally the builds should be reproducible. Otherwise, one of the main benefits of open-source software -- ability to verify its security -- is completely lost.
Fortunately, Flatpak != Flathub. There is also Fedora's flatpak repository and that's what I'm using. It doesn't have as many apps as Flathub, but their number is growing.
I prefer flatpaks to RPMs because of the sandboxing feature. While it's not perfect yet, I like that I can forbid most of my apps to access the network and to limit access to the filesystem and other system parts for apps that require network as much as possible. As a result, the trusted base of my system can be reduced significantly (and the base system can then use other method to confine its processes which on Fedora is SELinux).
Another benefit of Flatpak over traditional packaging systems is that it's a cross-distro package manager and the apps can be installed on any Linux distribution. Even if we end up with multiple Flatpak repositories like Flathub and Fedora Flatpaks with different approaches and philosophies, users of any Linux-based OS can then install apps from any repository they like, and OS developers can focus on the base system.
So in general I like Flatpak and I think it's a step in the right direction, but I can't say the same about Flathub. For me it's unacceptable to install anything from Flathub unless they fix their supply chain security flaws.