It’s going to confuse everyday users
Call me a conspiracy theorist, but I believe this is the intention. I think big companies deliberately put in confusing and bad design to "test the waters" and see if people will still buy their products. It's the same with the apple mouse charging on the bottom, or why companies keep making their logos uglier with each iteration. It's a psy-op to condition the masses into accepting worse products without complaining.
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.