Just a guess, but Windows executables probably depend on a bunch of Windows APIs that are guaranteed to be there, while Linux systems are much more modular and do not have a common, let alone stable ABI interface in the userspace. You can probably get small graphically capable binaries if you depend on QT and just assume it to be present, but Flatpak precisely does not do that and bundles all the dependencies to be independent from shared dependencies of the OS outside of its control. The article also mentions that AppImages can be smaller probably because they assume some common dependencies to be present.

And of course there are also tons of huge Windows software that come with all sorts of their own dependencies.

Edit: I think I somewhat misread your comment and progval is more spot on. On Linux you usually install software with a package manager that resolves dependencies and only installs the unsatisfied dependencies resulting in small install size for many cases while on Windows that is not really a thing and installers just package all the dependencies they cannot expect to be present and the portable version just does the same.