Since Brave is the company that developed and maintains the Flatpak version, I don't think they meant to imply that it isn't secure. Instead, I believe they meant that they didn't test the effectiveness of the Flatpak sandboxing.
As far as I'm aware, DEP/RPM packages are granting root system privileges, but Flatpak/Snaps are isolated, so theoretically, they should be safer. You can use tools like Flatseal to modify Flatpak permissions, granting access to local files if necessary (which is not permitted by default for security reasons).
Since you favor Fedora Linux, this could be useful:
I was wondering if someone could be kind enough to enlighten a new Linux user on the practical differences between installing an app as a Flatpak vs. installing as an RPM package. I’ve come across these two types of downloads while browsing apps on Fedora’s Software app, and I’ve seen that...
discussion.fedoraproject.org