The Flatpak needs very broad permissions over the Filesystem. Files launched from a File Manager can always be opened by an app, and "Ctrl+O" should invoke the Desktops xdg-portal for filepicker, mainly GNOME or KDE. This would allow users to restrict any storage permissions of Libreoffice and reduce attack surface. As the Flatpak is now officially supported and distros like RHEL are starting to deprecate their native packages, I think many people would be happy about this change!
Another reason may be mentioned at https://ask.libreoffice.org/t/103188/6 - seems like the integration dialogs lack some places, and Mozilla apps workaround that using xdg-desktop-portal filepicker.
yes, using a native portals always requires an app to have the same access as the filemanager, which is very complicated for Flatpaks. /mnt and more will probably be missing. Just using the native filepicker portal also has the convenience of having bookmarks shown, that the user uses anyways (at least in KDE), so it is always the same filepicker and a consistent experience. So this has huge UI benefits as well. It should be a small change to implement opening the portal instead of the filepicker.