Flatpak uses Portals to let the user grant access to different files/directories, apparently they don't have access by default: https://docs.flatpak.org/en/latest/sandbox-permissions.html

I was also unable to find any Flatpak that has access to the home directory when installed, you may well be right but I couldn't find any. I used Flatseal to verify the permissions: https://flathub.org/en/apps/com.github.tchx84.Flatseal

I'm also of the opinion that we generally shouldn't use software that we don't absolutely trust. That has kept my .bashrc (and other files) safe so far.

I don't think flatpak allows access to hidden files so even those with access $HOME cannot do this.