In my particular case: I don't want to wait months or even years for updates to arrive in my distribution. With the Flatpak version I get updates usually on the same day they are published, since the Flatpak is also maintained by the calculator developers, and I also get a calculator which can't access my ssh keys or the internet, due to sandboxing. And in case of any breakage, I can also quickly roll back to the last version.

Without flatpak I'd need to use some rolling release distribution, where not just a few applications get updated quickly, but also the rest of the system, which I'm not interested in.