Uh, no. Almost everything you can do for logical security only requires free software. Something as easy as ticking the box “encrypt my drive” and putting in a good password when installing Ubuntu or whatever is about as easy as it gets and is LUKS2 (“actual security”, as far as at-rest data encryption is concerned).
The literal way to read what you wrote is to never ask Flatpak, in order:
The only reason no one thinks this is what you mean is because of how many people also mess this up.