I haven't used any flatpacks, mostly because they don't seem to have a good solution for running terminal programs. (Also I don't like that the application developer chooses the permissions to expose rather than the user.
However, I have been using bubblewrap which is what flatpack uses under the hood to sandbox. This allows me to run both gui and non-gui programs, and I have the control of exposing the minimum required permissions that I'm comfortable giving an untrusted piece of software.
There's no way of knowing, which is the whole problem with their model and why a lot of us self host things in the first place. Even if they super duper promise not to use the data, they could be lying. And if they are actually true to their word today, that could change tomorrow.