Flatpaks hosted by Flathub are compiled by Github and are not meant to be modified by the user. So pip tends to be unusable for flatpaks in general. This is a security issue meant to protect flatpak users by having apps operate in a sandbox and not allowing flatpak apps or runtimes to be modified after being compiled. This is the downside of flatpaks for apps like Gramps that have a lot of customizations available which depends on a variety of additional prerequisites.
The Gramps flatpak has some extra dependencies compiled into the flatpak so that common addons can be used by users. The list of dependencies are in the ReadMe at GitHub - gramps-project/flatpak: Manifest and data files required to make a Gramps Flatpak If you want a dependency added to the Gramps flatpak, please post an issue at the Gramps Project flatpak repo at GitHub · Where software is built if you have a Github account, or at the Gramps bugtracker where someone could tag me.