this is sad

As it is, the flatpak variants are also strictly less useful. With a standard LO installation, I can easily use its filters from a script to convert weird document formats to something more usable. I can just install a JRE to unlock the remaining features. Does the latter work with the Flatpak? What would I need to go through to achieve the former?

LibreOffice is already the kind of software that's a pretty good match for what Flatpak can do. The utility of many other programs will be much more severely restricted when decoupled from the system.

Interaction with the system is a desired feature of most software. These are not smartphone apps. It's also the hard part of any sandboxing effort. Annoying the user with thousands of file picker dialogs is not going to cut it except for the most trivial of programs.