In 2006 the security landscape was very different. The common understanding of security being a tremendously subtle issue was much, much lower. A typical system from 2006 was much more trivially exploitable than one today. A lot of things can be said about security attitudes in 2006 vs now.
I can't see any real benefits to the Linux approach and never could. It's one of the reasons I ended up moving to macOS. There's hardly any malware there too and yet app developers build packages themselves.
>The world hasn't collapsed for [major OS vendors] so far
Hell yes it has. Malware and user-hostile is running rampant on the "major" platforms like Windows and macOS. Have you ever used a non-technical person's computer for a few minutes? It's like a warzone.
Personally, I think that says a lot about the Linux desktop and its community.
I have used non-technical people's Windows machines, and they were not a warzone. I've looked over the shoulder of plenty of other people using Windows & Mac computers, and generally not seen any obvious signs of malware infestation. There could be unseen malware lurking, but we can't assume that with no evidence.
Maybe this depends on the non-technical people you know, but it's definitely possible for people to use Windows/Mac computers and not be dropped in a pit of malware.
Do maintainers commonly audit source code to look for vulnerabilities? And at any rate, aren't the common security-critical libraries for flatpaks, like OpenSSL, already (in theory) provided and maintained by the runtimes?
All the major consumer OSs distinguish between system components, like cryptographic services and graphics libraries, and user-facing applications. The world hasn't collapsed for them so far, and in an ideal world that distinction allows for better delegation of responsibilities.