The flatpak version isn't created or maintained by Proton, hence why it has an unverified tag. Proton explicitly stated that it's been created by a community member, and it's not official in any way.
Whether you decide to use it depends upon your threat model. You can go look at the source for the flatpak and see if anything looks awry (like pulling source files from a forked repo, for example).
Another option is to use manual configurations. Scroll to the bottom of their help page and pick the one that fits your needs: