All scoop does is extract installers/archives from the applications own portable distributions, and then create shims for them. Scoop packages aren't actually packages. They are just manifests that point to a URL to the apps download, and a list of executables to make shims/shortcuts for and that is it.
There's the nonportable bucket for apps that have er.. nonportable versions.
I'm considering automating the conversion of my most used apps to MSIX, so they can get always installed in a clean way. That may break certain apps like Steam, which need to install outside the virtual FS, but I hear MSIX supports global registry an global FS access exceptions nowadays, so not all hope is lost.