Puerto Rico, 3-player: Which role order in the first round?
The first round is almost always:


Settler (P1:Quarry, P2:Corn(or Sugar if Corn unavailable), P3:Indigo (other choices are also good)
Builder (P2:Small Market or related production building, P3:Small Market, P1:Pass or (Small Market if available, sometimes Small Indigo)
Mayor (P3:Corn and Small Market, P1:Quarry, P2:doesn't matter)


An in depth analysis would take pages, but your two latter cases make no sense, because Craftsman gains Player 2 no advantage. Clearly, they could have chosen Builder, built the Small Market for free (1 VP), and prevent Player 1 from getting the opportunity to build it for free with a covered Quarry.

If Player 1 chooses Mayor, Captain, Craftsman, or Trader then no choices can be made so I won't cover those. If Player 1 chooses Builder, Player 2 should build either Small Market or Small Indigo, Player 3 should probably build Small Market. This gives Player 2 the opportunity to get the first Quarry by selecting Settler (cash is king in the early game), or Mayor to cover both Indigo slots. If they choose wisely though, that would leave Player 3 with Mayor, covering their Corn+Small Market.