To be clear, there will still be a deb package of gnome-software in the archive that can be installed. It will be installed as a dependency if you install gnome-software-plugin-flatpak. If you choose to do that, you will have two versions of gnome-software installed, but that is not the out of box experience. I think advanced users that choose to do that will understand why there are two versions.
The deb version of gnome-software will no longer be called “Ubuntu Software”, we will remove that branding. This should prevent confusion.