I believe it's showing the payload only for the portions needed to download and run. Flatpaks may have other dependencies that are met by other installs, and won't redownload what is already present afaik.
So if Minetest as a full install is 1.6MB, but you already have all the other dependency pieces already installed, it just downloads the 5.8KB missing, meaning the runtime of Minetest is that 5.8, and the rest is dependencies.