I'm not too sure about "falling behind Windows", personally. The major lines of defense that Windows appears to rely on are code signing and a signature database, with behavioral AV being a relatively recent creation that still doesn't cover a lot of big holes. (for instance: What if I manage to fake my way through an OV/EV cert or use a leaked one? What if I use polymorphic code obfuscation that can generate hundreds of different signatures, but is also used by "legitimate" programs as DRM?) There's SafeSearch, but many people just click past those warnings anyway.

It's just as easy for a Windows .exe to create a service that runs when you log in as it is for a Linux app to write something to .bashrc - so its not a uniquely Linux problem.

macOS has the big Apple hammer to force developers to comply - Apple has the power to say "from this release on, all permissions need to be requested for or they won't work". Comparing the two companies, Apple uses the big hammer they have to force some compliance from app devs, while Microsoft often tries not to break stuff.

Linux doesn't have a big, central hammer like Apple does, so progress like Flatpak's isolation has to happen in steps, or else you end up in this chicken and egg problem:

- App devs won't support Flatpak with stuff like using portals because Flatpak has a small userbase - Users won't use Flatpak because it doesn't have apps that they want, and will instead go about doing things the old way

This "we'll give them $HOME for now and let them fix it eventually" is deliberate - you need to drive adoption for Flatpak before apps consider adding special code paths for it. The goal is to eventually fade out $HOME access or severely restrict it, but unfortunately this is the norm.

I've mentioned this on other posts, but this is deliberately why Flatpak's messaging on their website[0] is focused on ease of distribution instead of security. In addition, if you feel like you can put up with an app having a restricted view of the filesystem (for example, you don't think you'll touch anything outside ~/Documents/Models with Blender), you can adjust the sandbox to fit your needs.

[0]: https://flatpak.org/