OSs need to stop letting applications have a free reign of all the files on the file system by default. Some apps come with apparmor/selinux profiles and firejail is also a solution. But the UX needs to change.
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All except macOS let anything running as your uid read and write all of your user’s files.
This is how ransomware works.
It's much like an Android application, except it can feel a little kludgy because not every application seems to realize it's sandboxed. If you click save, silent failure because it didn't have write access there isn't very user friendly.
In my case, I either use apt (pipx for yt-dlp), or use a VM.
As an administrator, I'm constantly being asked by developers for sudo permission so they can "install dependencies" and my first answer is "install it in your home directory" sure it's a bit more complexity to set up your PATH and LD_LIBRARY_PATH but you're earning a six-figure salary, figure it out.
I use it all the time, but I'm still looking for people to review its security.
There are solutions on the desktop like Qubes (but it uses virtualization and is slow, also very complex for the average user). There are also user-space solutions like Firejail, bubblewrap, AppArmor, which all have their own quirks and varying levels of compatibility and support. You also have things like OpenSnitch which are helpful only for isolating networking capabilities of programs. One problem is that most users don't want to spend days configuring the capabilities for each program on their system. So any such solution needs profiles for common apps which are constantly maintained and updated.
I'm somewhat surprised that the current state of the world on the desktop is just _so_ bad, but I think the problem at its core is very hard and the financial incentives to solve it are not there.
A locked door is better than an unlocked one, even if it gives its owner a false sense of security. There is still non-zero utility there.