The virt-manager flatpak doesn’t work out of the box, you need to do some setup on the host. At that point you may as well use the deb of virt-manager.

If you install virt-manager on Debian via apt it will have full system acres and also automatically install and configure libvirt, so this method is preferred.

Is there now a flatpak for virt-manager?

Depends on what distro you’re on? You say the deb version is 4.0 and flatpak is 5.0, suggesting you may be on a long release distro?

I’d favour the Deb version as it’s official for your distro. The flatpak version is unverified; it’s extremely unlikely Virt-Manager is compromised or will cause any issues but virtual machines do have security risks.

Also problem solving issues with the flatpak version may be more difficult as you have a whole layer potential issues in the sandbox on top of all the other issues people can have around KVM/QEMU. But you could install it, if it works great, if not, revert to the Deb version.