The Flatpak is indeed community-maintained. That, combined with the fact that I haven’t used it myself, means I can’t say much about it. However, its current maintainer/packager has contributed a few patches to various parts of Jami, which were helpful and much appreciated. That might say something about their attitude towards Jami and free/libre software in general.
It appears that the repository for the package definition is at https://github.com/flathub/net.jami.Jami, and from what I can tell, it’s fairly active and up-to-date. So you could give it a shot if you like, and find out for yourself. Also since the package definition are publicly available and from what I can tell freely licensed under the GPLv3+ like Jami itself, you could clone the repository and try building the flatpak yourself.
Hope this helps.