If I hand you an electron that passed through a double-slit, can you tell me which slit it went through? What you should be able to do, however, is set up an experiment which shows that it did not just go through one or the other. It did, in fact, go through both slits. E.g. Delayed Choice Quantum Eraser.
Similarly, it is possible to set up an experiment that shows absolutely definitively that the atom is neither in the state having emitted zero nor one photon. It's somewhere in between.
Now, for the photon itself, you can try to interpret it in different ways. You can try to pretend that superposition is just some voodoo. But that doesn't work with the atom. As demonstrated prior, the actual charge density, which is an observable, of atom in transition is distinct from either ground state or excited state. As further demonstrated, the dipole moment is present and can be measured.
This, in turn presents an excellent opportunity to cut through the Gordian knot you present above. Say, rather than make measurement that tells me which energy state the atom is in, I do measure the electric dipole of the atom you handed me. Say I get a non-zero result. That would indicate that the state has collapsed into something that is neither the ground nor excited state. Having conducted that measurement, I can tell you exactly what fraction of the photon has been emitted. Naturally, this measurement is still a product of collapse, so I don't reveal information about what that fraction was originally. And nonetheless, I can make a measurement that gives me an answer that is a fraction.