Hi Giovanni,
Yes, microphone placement for recording organs is one of the most contested subjects in the recording industry, I think!
Some of it is just a matter of personal taste, I think. At a live performance, people can just sit in the seats that yield the sound they like, whereas for a recording, the engineer has a make a decision that everyone has to live with.
Besides finding a spot that gives a nice balance of reverb and presence of sound, there often exist one or more spots where the sound "blooms" as you described. The weird thing about it is that often these microphone spots are in places no one could ever sit, like many feet off the floor. Then you're left wondering if you should use this placement as no one would ever hear it this way in person. But it might sound really good. . .
I will usually go for the good sound, because I am definately one who believes the art of recording music is different than live performance. To my ears, attempting to reproduce a live performance rarely is satisfying in the long run; so to me, recording needs to be approached as a different art, much like the difference between stage acting and acting for TV cameras.
A votre sante!
Tom