There is no reason to distinguish between cases 1 and 2, since the fundamental physics is the same.
The times of both processes are very different.
The first process: the atom is slowly decaying, it can take billions of years, but will decay eventually. Individual atoms have different times of decay and we cannot predict it now.
The second process begins when the atom has decayed into some other particles and these enter the detector and trigger the detection process in it. This is very fast, <milliseconds or so.
It is most natural to think that these are two different processes. If the Copenhagen explanation of the formalism does not distinguish them, I think so much worse for the tenability of that explanation.
The way that I would think of the process is as before. If at time t1 we measure an H-atom in the state 2p and at time t2 we find it in the 1s state, we know that the decay happened at some time in between and it was instantaneous.
I do not think one can measure which electronic state the atom is in. The 1s, 2p symbols only refer to terms of optical spectra, or eigenfunctions of Schroedinger's equation, but not to results of measurement of the state. Such measurement could be done by measuring X-rays scattered by the electron in the atom, but this would necessarily perturb the atom so much that its state would be far away from what it is in natural conditions (it would ionize).
I may be mistaken; do you have some reference to a paper which deals with direct measurement of electronic states?
What we can do is to resolve light radiated/scattered by the atoms. If one measure this, many features of the spectra (splitting in el./mag. field, sharpness of lines) is well explained by Schroedinger's wave mechanics, with no need to introduce instantaneous Copenhagen jumps.
There are transitions, but there is solid evidence that they are gradual - coherence time of 1s-2p line is 1 ns, interference and dispersion phenomena, ...
But let us suppose the electron really have jumped instantaneously from 2p to 1s state and radiated photon of frequency f = \frac{E_{2p} - E_{1s}}{h}.
Now what the frequency of the photon means if the process was instantaneous ?!
The frequency of radiation can only be defined within 1 ns coherence time if the wave has at least this extent. So the radiation has to be produced at least for 1 ns.
How can you explain the coherence of the radiated wave and preserve instantaneity of the transition? This was and is a serious problem for theory with instantaneous jumps.