Realistically, I know that I do not have the skills to evaluate complicated applications and their complicated dependencies for security characteristics, so I am 100% reliant on packagers, maintainers, etc. for my security anyway. I'd rather just donate to the people publishing and maintaining the packages and hope that they are doing the job well, than fruitlessly attempt to fuss over it myself.
The good news is there is a solution to this. The trusted system shows a file picker, and then grants access to the sandboxes application.
This is called the File Chooser Portal. https://docs.flatpak.org/en/latest/portal-api-reference.html...
I suppose additional security features inspired by mobile systems couldn't hurt either. Like a pop-up whenever something accesses the clipboard.
I just hope flatpak sandboxing works well...