That was already the normal long before flatpak. Installing the same packages with your distro package manager will also install the same several gigabytes. The number you see in flatpak might be an illusion though, the real amount of space taken up on disk is less:
https://blogs.gnome.org/wjjt/2021/11/24/on-flatpak-disk-usag...So flatpak may actually be a solution to the problem that you don't realize. It can only cause a big issue if you have a lot of old software that never updates the runtime.
