Official (.deb/.rpm) is better for email security.
I use Ubuntu so can use .deb, but I prefer to use Flatpak’s only. However, using an unofficial package for something as important as email account makes me nervous.
Purely looking at the packaging formats themselves, flatpak offers better security than .deb (excluding Web Browsers). Specifically its sandboxing (if sufficiently/restrictively configured) protects against a malicious or infected app attacking more parts of your system. The data inside the sandbox, in this case your emails/calendar/account data, would generally not be better protected.
However, in this case the flatpak is less trusted because it doesn’t come from the official developer, which ootb means that you’d have to trust an additional party, which is generally worse. Specifically it means you’d have to
trust the maintainers to not be actively malicious
trust them to not accidentally lower security by introducing new vulnerabilities
trust them to not accidentally indirectly lower security by breaking features that conflict with flatpaks sandboxing, which the app wasn’t originally developed for
trust them to (reliably) update as soon as possible after the official package does, so you’re not vulnerable to known exploits that are already fixed in the official application
on a lesser note, trust flatpak devs and maintainers of other additional packages to not contain/fall victim to supply chain attacks
Which is better depends on your threat model, as the two options have positives and negatives affecting security in different ways and scenarios.
My personal solution is to use all Proton apps as Web Apps of a dedicated Flatpak Browser, which I’ve optimized to only run these specific sites and don’t use for anything else. This means I’m not trusting any unverified devs, sidestep the disadvantages of flatpak browsers and still benefit from general flatpak advantages. My DE is GNOME and my Browser is GNOME Web, so I’m not even trusting any additional parties. Until Proton hopefully eventually officially takes over the Flatpaks, I can recommend this solution, even if it’s a little sad not to be able to use the actual app.