Those who are inland, are there because that was where the biggest native centre of population was, being mexico city the best example. Spain conquered those lands, but they didn’t kill the local population and rebuild from zero (as the english did up north). The Castilian just took their capital, and made it the capital of the region, keeping the same commercial activities, and adding the ones that came from Spain with them. Spain just didn't have the money to protect all of its colonies so they built the big cities inland where possible.