Is it that it's a quantum-scale effect, creating a truly identical system at each cycle, as opposed to the approximate classical-scale system of a conventional oscillator?
To give a music analogy, the constraint is like always play the same chord on the first beat of each measure. In between you are free to play whatever chords you like.
How does a physical system can acquire such property? I have no idea that's the mystery a physicist will have to explain.
I get your idea of using various periods : If instead of a sum of periodic signals, you do something completely nonphysical like a product cos(x)cos(x/3)cos(x/5)cos(x/7)any_f(x) you can observe indeed that the zero crossings come back periodically. (Edit: something kind of an amplitude modulation may not be so nonphysical after all)
Mapping it to spatial terms, I think: You could take a bag of beans and lay them out in a nice repeating grid pattern if you want, giving them spatial symmetry. But you have to keep making the grid yourself. The "bean crystal" does not naturally spread on its own. When a real crystal cools, the entire substance aligns into a regular repeating pattern on its own without any external force needed.