The question has come up before and no-one seems to know.
As the tapers are precision made I'm confident that the odd angles are deliberate, not an accidental by-product of the way they were machined or calculated.
My guess is that Morse deliberately used a variety of slightly strange angles as a way of detecting patent infringements. At the time quick change tools were an important innovation and the Morse company would want to protect their idea for as long as possible. A Morse taper cannot be independently reinvented; anything to those specs not made by Morse must be a copy, and I think it would be easy to convince a court that the patent was infringed.
Accidental by-products do occur in measurements. Careful analysis of the dimensions of the Pyramids seem to prove conclusively that the Ancient Egyptians must have calculated an accurate value for π, 3.14159… This is a serious shocker, because it means their mathematical methods must have been far more advanced than other evidence suggests. Actually π emerges from the data because the Egyptians often measured distances with a device like a surveyors road wheel. And wheels naturally come with π, it's not a design requirement. π in Ancient Egypt is coincidence, not genius.
Dave