There's no reason for a flatpak application to load slower than a 'native' application. It just namespacing[0] to separate the application Do you have measurements?

Snap seems to be deeply flawed however. They use compressed files to store things that need to be mounted when one wants to run an application[1].

[0] https://github.com/containers/bubblewrap [1] https://www.freecodecamp.org/news/managing-ubuntu-snaps/