Single expansion three cylinder engines did have their crankpins set at 120 degrees, or more correctly had their valves set at 120 degrees. The center crank would be off 120 degrees by the amount that the center cylinder was inclined above horizontal. Here is what ICS had to say.
Baldwin's #60,000 was the exception, being a compound with the the center cylinder being the HP, her outside, low pressure crankpins are set at 90 degrees so she gave four even exhausts per revolution. Her HP cylinder produced less horsepower than the LP's, dropping off to nearly no horsepower as she was notched up, so maybe that's how they got away with the uneven turning force.
One detail that would make a single expansion three cylinder locomotive sound offbeat even when in good repair was that the center cylinders were often smaller than the outside cylinders due to space constraints, so held less steam to exhaust.