The harlequin "phenomenon" came about because of genetic mutations that arose during mericloning. The process was thought to produce clones genetically identical to the mother plant, but it's since been found that this isn't always the case. In the early 80s, the Brother nursery came out with a clone called Golden Peoker 'Brother' that they wanted to produce in quantity. The flowers were white, with randomly spaced dark magenta spots that were more concentrated at the center. So they mericloned it. Some of the clones came out as duplicates, but others were mutated. They took the mutated plants and mericloned those, repeating the process with the "offspring" which themselves were mutated, over and over, with each succeeding generation. They finally ended up with flowers that were predominantly white, with large, raised, cranberry-colored blotches.
Problem was, each spike produced very few flowers--two, maybe three--but by breeding those with plants that had many flowers on the spike, they've been able to increase the flower count. They're still not as abundant as those on a non-harlequin, but it's getting a lot better: Everspring Prince and Everspring King can be absolutely stunning examples.
Interesting side-note, the blotchiness can be directly affected by the temperature under which the buds have developed. Under warm conditions, the blotches on some of the clones will disintegrate into a haze of spots. Under cool conditions, they'll coalesce into the distinctive "harlequin" pattern. Since Phal flowers can last a very long time, those clones will "revert" depending on the season, developing one spike of flowers with random, tiny dots, while their newest spike will have flowers showing the raised, harlequin blotches. They can be so different that it's sometimes very hard to believe that both spikes arose from the same plant.
I don't know nearly enough about genetics to understand or begin to explain why mutations occur during mericloning, but if someone wants to take up the ball and explain that in more detail, please do!