I would suggest that your "Basic Colonist Training Package" work something like Background Skills.
The Players can select from one of the skill packages and get Level 0 in 1+Edu DM different skills.
So most colonists would get 1 Level 0 skill, while a highly educated one might get 4.
Then if the character works at it, they could increase their skill to Level 1 or above using the normal learning methods.
Since the Players are going to know the type of world they will be colonizing, they can taylor their skill selections to better improve these types of skills, so they may not need the basic skill package as much as your NPCs.