It conflicts with the browsers own sandboxing and Flatpaks aren’t necessarily created by the package or distro maintainer. You are placing trust in an intermediary.
I can’t say for sure, but I will note that just because chromium is generally regarded as having better sandboxing than Firefox and friends, that doesn’t mean they don’t have sandboxing. I would still expect any modern browser to have some degree of sandboxing, and I would almost certainly expect it to be better than what Flatpak offers. (I am by no means well-versed in this area, though.)
Keep your browser up to date, minimize extension installation/use, and don’t click things you can’t trust. If your threat model demands more than that, a Flatpak probably isn’t going to help you much. I’d say start using VMs/Qubes/Trivalent via secureblue (and follow the previous advice regardless).