This might be hard to explain, but I'll try!
Both Dolby Atmos and the Realiser (should) use a microphone during setup to analyze a performance. This only needs to be done during setup, and Atmos' setup process would have figured out how to indicate positional angles before you would begin setting up the Realiser.
Think of channels as directions, not as speakers. Dolby Atmos can have MANY speakers, while headphones have two speakers, so for our purposes the quantity of speakers isn't very important. What is important is directions. Atmos receives raw positional coordinate data, and because it understands where the speakers are located Atmos computes which blend of speakers to activate in order for the audience to perceive sound coming from a particular direction. Atmos does this live instead of pre-encoded to a certain number of channels, because that's the only way it can account for a custom quantity of speakers as in your German theater example.
The Realiser "says" to the theater with Atmos, "Ok, great, now that Atmos has figured that out, play sounds from these 16 directions I tell you and I'll record what that sounds like in the ears of my owner, my audience of one." If I recall correctly, the A16 was named that because it can replicate up to 16 channels, not 12. So, when you bring the Realiser back home or wherever, the Realiser "looks like" an evenly placed 16 speaker-channel Atmos setup to your Atmos source.
Now, a completely object-based audio format from start to finish (like OpenAL, used in some PC games like Unreal Tournament, Bioshock, some of the Battlefield games, but unfortunately seems to be dead now) with PRIR customization would be the ideal holy grail in my opinion. The vast majority of content just doesn't output sound that way right now, so the Realiser is the next best thing, and it's fully compatible with legacy 5.1 and stereo content. Some day, full Virtual Reality may change that, but for now the Realiser still creates a convincing virtual theater experience.