It's not about that, it's about why most of the English speaking countries have dealt with racial segregation and racism is still a big issue there.
- - - Updated - - -
You definitely haven't got a clue about this topic. Besides, the Encomienda model didn't last for long and by the 16th century was almost over. You don't know how the Spanish Empired was ruled nor how its administration evolved, do you?
By the way, you talked about outrighting an entire population. Who did that? Please, tell me. Because if you're talking about the Spanish Empire, you're the most ignorant person I've ever seen in a long, long time.