It only applies to citizens or permanent residents. I assume that the huge difference in qualifying points earned in every country is to be more competitive in markets where LATAM isn't the top dog. In Colombia, for instance, they compete hard against Avianca. So making it easy to achieve the top categories might be attractive for local flyers. On top of that, due to Colombia’s geography and poor road infrastructure, Colombians prefer to fly from one city to another.
The competition in Brazil is huge as well.

On the other hand, like Chile, i.e., LATAM dominates the market by far and has massive contracts with mining companies. They don't need to lower the bar for flyers to achieve top tiers categories in order to be chosen.

At the end of the day, (like every business), everything comes down to profit and make money more than anything else.