Like a .deb package, a flatpak can be made by anybody and can contain free software and/or proprietary software. In the present case, the Gajim team makes the flatpak and I see no reason why it would not be all free software (since Gajim and its dependencies are free software): https://dev.gajim.org/gajim/gajim/blob/master/flatpak/org.gajim.Gajim.yaml

... but flatpak itself is not packaged in Trisquel 8.

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