I expect the Flatpak sandbox to protect my ~/ from getting cluttered by applications, not to protect me from any actually malicious software. The post's premise seems misguided.
YES. I don't understand this delusion people keep perpetuating. Flatpak has a MILD form of container sandboxing. For a real security sandbox we have Firejails or Bubble wrap.
Flatpak is, at it's core, a software development and distribution packaging format. NOT a security implementation.
I always check my flatpak settings post install before running the app and adjust permissions according to need. I mean it does offer more security to me since it's user installed, I can granularly update permissions and control more or less where and what is can touch.
Alternatives to this are SELinux,AppArmour and firejails which are slightly more inconvenient to use.
To me that is mostly secure,or secure enough.
Well and then there's some immutable distros which might help overall.
If we admit that then an app store where anyone can create an account and upload software becomes extremely problematic. This is especially true wherein clients autoupgrade very quickly.
Step one. Legit package a popular app
Step two. Wait for substantial uptake
Step three. Mix in some ad or malware and watch a tens of thousands get instantly owned.
I ignored flatpaks long enough, as everything could be installed as packages, without additional GBs of dependencies/libraries/runtimes of flatpaks, that duplicate the system ones. Recently started using immutable system, which assumes flatpaks is primary way to install apps. I found it is incredibly convenient when all your apps put their data in a single place, easier to backup and system looks clean without bunch of shit, apps create where they want.
In addition to own new code, bundled copies of libraries in packages introduces net new attack surface which isn't patched via the regular distribution security patch process. The image decoding lib that allows remote code execution now exists in flatpaks independently from the one in /lib. Every flatpak vendor that contains it has to build and ship their own patched version of it. This is even more valid for any other libraries flatpaks include that don't exist on the system. The most widely used Linux OSes come with security patching processes, expectations and sometimes guarantees. This new attack surface breaks those and the solution is security sandboxing. This approach has been proven in mobile app packaging and distribution systems. Android is a great example where apps are not trusted by default and vulnerable ones rarely cause collateral damage on otherwise up-to-date Android systems. This is an objective problem with the out-of-band distribution model allowed by flatpak and snap or any similar system, whether you care about it or not personally. It's a well understood tradeoff in software development. It has to be addressed as adoption grows or we risk reducing Linux security to the levels of Windows where apps regularly bundle dependencies with no sandboxing whatsoever.
All Flatpaks are portable. There is no reason to use their repo usually though as Flathub often has more up to date, featureful, or upstream maintained versions instead.