This is especially bad for projects like Linphone (open source SIP Client) which exclusively provide Flatpak-builds for Linux [1].
[1]: http://www.linphone.org/technical-corner/linphone/downloads
[1]: http://www.linphone.org/technical-corner/linphone/downloads
The nice thing about flatpak for a phone is that it could in the future offer something like the Android/iOS permissions interface.
So maybe this is not an inherent problem of this technology and will work better in the future.