But to what extent ? Was it about pushing the borders a few miles East or North to include a couple cities, or about all-out conquest of territories the size of EU4 provinces ?
That being said, I agree with you that the game fails to model how difficult it could be to pierce geographical borders. It's the same thing for the Caucasus, the local countries have increased coring cost because the game can't model the pain it was to control the area militarily.
Besides, I've never seen a colonial nation going independent in the XVIth century. Usually, the biggest Portuguese colonies sit at 100% liberty desire (OK, that's a problem, I agree with you) for 250 years. Sometimes, they win their independence war in the late game because somebody helped them getting more than just +25 ticking warscore (and a lot of negative warscore from naval battles).