This is a very interesting question, since the gain staging in the Prophet 12 is a quite important aspect of the synth.
Others with more experience making patches for it might very well have a different view, but to me it is much more important to consider the amplitude response in the earlier stages of the signal path: the oscillator, character and filter stages.
There is quite a lot of headroom along the way, and the level of the signal going into the filters has a huge influence on the harmonic content of the final sound. It has been established in several discussions that many who complain that this synth sounds harsh and non-appealing to them have been using a rather high input level into the filters, and that by reducing the oscillator levels the sound becomes much softer.
This effect is so large, that I have not even considered any effect the final output stage might have. Again, others who have spent more time recording the output from this synth might have a more informed opinion.
The fact that you find that different patches have different output levels reflects that the creators of the patches utilised this aspect of the synth. Does this difference perhaps mean that there is not a universally best master volume level?
I am sorry that this doesn't really answer your question, if you only want to record presets at the best quality, and not create your own patches.