GNOME Software needs to work across all distros, including those that aren’t DNF-based, so to do anything like this they would presumably want a package manager-agnostic approach.
I see where you’re coming from with this: a software manager that would manage both individual packages, as well as apps (be it package-based on not). IMO there are a couple of barriers in this request:
These are separate projects with different aims. It’s as if one would ask the merger of Thunderbird with Evolution. Not really realistic. A more sensible approach would be to pick one project (e.g. GNOME Software), and define what are those features in the other project that you would like to see in the first one (e.g. package-level management). Then file them as a feature request with the upstream project. What would result though is not a small, actionable item, but rather a fundamental change. I doubt such a request would resonate with those doing the actual work (maintainers, contributors).
The interest for such a complex app is rather low. While GNOME Software is generally used by the wider audience, those advanced users who want/need to manage package-based installations usually revert to the command line, where dnf CLI provides a rather powerful tool.
Separating application/software management via GUI apps such as GNOME Software from package management via CLI tools has proven over the years to be the more wise approach. Putting package management into GNOME Software would IMO only bring confusion and no real gain to the less experienced users, who would not know how to handle the outputs of a search result.