Maybe by the makers of flatpak, maybe by the app developers
This falls on the app developers. They’re supposed to be using something called XDG desktop portals. It opens a filepicker window on the host, the user selects which file they want, and that specific file gets passed through into the sandbox automatically, no permissions needed. Though it’s not perfect either – AFAIK there’s no way to pass though a directory using XDG portal, and drag-and-drop is broken (at least on X11). For command-line apps (tho it’s not really what flatpak was designed for), the equivalent is the --file-forwarding
option.
A lot of “hardware raid” is just a separate controller doing software raid. I thought I lost access to a bunch of data when my raid controller died, before I realized that I could just plug the disks directly into the computer and mount them with mdadm. But yes, hardware raid seems a bit pointless nowadays.