I'm not sure of a different storyline with Alex being Scott's father. I wouldn't doubt it with all of the time/dimension changes they have made in the past.
But, the most consistant part of the Summers family, is that Scott is Alex's older brother and they were in an airplane with his parents flying over the ocean when the plane caught fire.
Then, they were pushed out of it by Scott's father, with only one parachute between them and it caught fire as they were falling.
They were rescued and put in an orphanage. Alex was adopted, while Scott stayed until Prof-X found him after he ran away from the orphanage.
Scott and Alex reunited soon after, I believe.
Corsair of the Starjammers is their father, while their mother died while giving birth to Gabriel Summers (Vulcan).