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Discover should allow to install deb files on rpm based distribution and vice-versa.

I don't know there exists distribution ID in packages, but if it does, then Discover can install minimal distribution version and install software in installed container.
For example I'm Ubuntu user and decided to install some rpm package for OpenSuSE, so Discover will download zypper/rpm and bash for OpenSuSE, build rpm database and install target package. After installation completes, Discover will extract information from Desktop files and create desktop files in parent system. Additional you can allow to restrict possibility of run software in some container by creating group of users for each container.

I think Discover should integrate with systemd-nspawn.

Installing packages built for another distro should only ever be done with caution by someone who knows what they are doing, and as such I think it not a good idea to add such functionality to Discover.

Instead it would be better to look into snap/flatpak/appimage packages provided by the maintainer of the package which come with such built-in container-like security (and which Discover should already support or be receiving support for soon).

Flatpak and snap are already supported. A backend needs to be installed which is not by default at least for kubuntu, I don't know about other distros. The packages are called plasma-discover-flatpak-backend and plasma-discover-snap-backend. I don't really like snap so don't use it but the flatpak integration works great.

The difference between an rpm package and a a deb package are more than just two different file formats.
The worth of a package is only party what it contains. Equally important is how things have been packaged and especially what meta information has been provided and checked. That is something this approach cannot honor in any way. Which basically means that it would jeopardize the wonderful advantages of a working software management system.
Not a good idea...