The cross-class skills aren't about being realistic. If we were trying to be realistic, we'd junk the class/level system altogether and go with a points based system where you buy all your character's abilities, like hero system or gurps.
Cross-Class skills are all about play balance, where a character's strengths in one area are countered by weaknesses in another to keep everyone on a more or less even footing. In most cases, your scientist class character who wants to be a pilot should multi-class into a class that gets pilot as a class skill and put his points there if he wants to be a professional pilot.
As I understand it though, this does not work for the Technomage who cannot multiclass. Can someone who has read the rules confirm that?
So, your Doctor (Scientist Class) wants to learn how to fly a Starfury. He goes to his buddy, Commander Sheridan, and says, "John, I'd love to get qualified in one of those new Thunderbolts." John, with eyebrow raised, says "Okay, Doc." He takes him down to the hanger and after a few weeks of training has him qualified. The character takes a level in officer and spend the skill points on pilot.
The other option, of course, is to use a feat. In this case, your doctor could have used that time to improve his skills as a doctor. He could have taken a medical feat of some sort, etc. Instead, he chose to forego that and become a pilot. He takes the Hobby Feat and can now become a piloting god, at the expense of not being quite as good a doctor as he could have been if he hadn't spent all that time learning to climb and bank.