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.